mtGenome Sequencing of NIST Reference Materials and ... · NIST Standard Reference Materials (SRMs)...
Transcript of mtGenome Sequencing of NIST Reference Materials and ... · NIST Standard Reference Materials (SRMs)...
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mtGenome Sequencing of NIST Reference Materials and
Population SamplesKevin Kiesler, M.S.
Research Biologist - NIST Applied Genetics GroupISHI Workshop: The Future is Now for MPS mtDNA Analysis
September 24, 2018
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Outline
• Reference materials and mtDNA sequencing
• Population scale sequencing
• Informatics
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First – the Disclaimer
• Disclaimer - Points of view in this document are those of the authors and do not necessarily represent the official position or policies of the U.S. Department of Commerce or the Department of Justice. Certain commercial equipment, instruments, and materials are identified in order to specify experimental procedures as completely as possible. In no case does such identification imply a recommendation or endorsement by NIST, nor does it imply that any of the materials, instruments, or equipment identified are necessarily the best available for the purpose.
• All work presented has been reviewed and approved by the NIST Human Subjects Protections Office.
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What is this?
A) Time machineB) Water purifierC) Steam locomotiveD) Mass spectrometer
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What is this?
The PLEX-IDFrom Abbott Molecular& Ibis BiosciencesSample plates stack here
Sample purification goes on inside here
The mass spectrometersits inside here
NIST evaluated this system in 2012 for potential “rapid, simple” mtDNA analysis
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mtDNA by Mass Spectrometry
• PCR across HV1/HV2/HV3• Eight tri-plex reactions = 24 amplicons
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mtDNA by Mass Spec
• Desalt PCR products (automated)• Electrospray injected Time-of-Flight (ESI-TOF) mass spectrometer
• Review data for “trouble”• Sodium adducts, overlapping peaks, etc.
• Compare to database• Known mtDNA types• Masses of PCR products
• Predict DNA sequence• Paper: compared with Sanger
• n = 711 samples• 99.97 % concordant
Outcome: Simplified, faster workflowAlmost as informative as Sanger
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NIST Standard Reference Materials (SRMs)
• ISO/Guide 30:2015• Reference materials (RMs) and certified reference materials (CRMs) (defined in 2.1 and 2.2)
are widely used for the calibration of measuring apparatus, for the evaluation of measurement procedures and for the internal or external quality control of measurementsand laboratories.
• Assess a new technology - calibration• Evaluate a method - implementation
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NIST Mitochondrial Sequencing SRMs
• SRM 2392• Three components
• Component A: DNA from cell line CHR• Component B: DNA from cell line 9947A• Component C: Cloned fragment from HV1 region of CHR containing C-stretch
• SRM 2392-I• One component
• DNA from cell line HL60
• Characterized with Sanger methods• Released in 2001
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Assessing NGS Using Reference Materials
• In 2012, all we had was a SOLiD system…• Sequencing by Oligonucleotide Ligation and Detection (SOLiD)
• Ligation chemistry based (it’s complicated) system for whole human genomes
• Very high coverage mtGenome sequence• ~ 45,000 X
https://www.slideshare.net/PaoloDametto/new-generation-sequencing-technologies
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All the Sanger-Based Information Checked Out
√√√√XXX√√
√√√√√√√√√√√√
There was no software available thatcorrectly handled these C-stretchinsertions with forensic nomenclature.
Reference material
Technology
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We Could Detect Some New Features!
• Heteroplasmy below what we can see with Sanger methods
SRM 2392 Component A (CHR)Position 1,393 R (17 % A)
SRM 2392-I (HL-60)Position 2,445 Y (7 % C)
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We Sent Some Samples to Service Labs, Friends
• Beckman Genomics sequencing service• Seven mtGenomes One lane on a HiSeq
• ≈ 40,000 X coverage!!! (≈ 3 to 4 million bases each)• Too much to display in IGV (not enough RAM)
• Edge Bioserv (Gaithersburg, MD)• Ion Torrent Personal Genome Machine (PGM) in 2013
• Seven mtGenomes on a 314 chip• ≈ 200 X to 400 X coverage
• Illumina MiSeq in 2013• Seven mtGenomes on 2 x 150 v2 chemistry• ≈ 10,000 X to 20,000 X coverage
• Children’s National Hospital (in collaboration)• Pacific Biosystems RS in 2014
• Long-read technology, low coverage• Some variants missed
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Then We Got Some Desktop Sequencers of Our Own• Ion Torrent PGM
• September 2012• Chemistry improvements over time
• 200 bp, 300 bp, 400 bp, HiQ
• Illumina MiSeq• September 2013• Chemistry improvements over time
• V2 2x150 bp, V2 2x250 bp, V3 2x300 bp
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Multiple Orthogonal Measurements
• Great approach for certifying reference materials!
SRM 2392Component
A Component B SRM 2392-INucleotide 64 T 1393 A 7861 C 2445 5149PGM Edge 26.8 21.2 72.7 10.6 5.1PGM NIST 1 24.3 15.6 45.0 7.5 9.1PGM NIST 2 25.0 17.5 65.7 7.7 7.7PGM NIST 3 29.7 16.5 59.4 7.7 7.7PGM NIST HiQ 33.2 15.2 77.7 7.7 8.4MiSeq Edge 33.0 19.0 87.4 10.7 6.8MiSeq NIST 31.6 17.9 88.4 9.1 6.4HiSeq BC 30.6 16.9 88.3 7.4 7.1SOLiD NIST 29.0 16.7 87.3 7.3 7.0Average 29.2 17.4 74.6 8.4 7.3St. Dev. 3.1 1.7 14.5 1.3 1.1
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Multiple Orthogonal Measurements
• Great approach for characterizing reference materials!
SRM 2392Component
A Component B SRM 2392-INucleotide 64 T 1393 A 7861 C 2445 5149PGM Edge 26.8 21.2 72.7 10.6 5.1PGM NIST 1 24.3 15.6 45.0 7.5 9.1PGM NIST 2 25.0 17.5 65.7 7.7 7.7PGM NIST 3 29.7 16.5 59.4 7.7 7.7PGM NIST HiQ 33.2 15.2 77.7 7.7 8.4MiSeq Edge 33.0 19.0 87.4 10.7 6.8MiSeq NIST 31.6 17.9 88.4 9.1 6.4HiSeq BC 30.6 16.9 88.3 7.4 7.1SOLiD NIST 29.0 16.7 87.3 7.3 7.0Average 29.2 17.4 74.6 8.4 7.3St. Dev. 3.1 1.7 14.5 1.3 1.1
87 %
It can also educate you about your technology.
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Multiple Orthogonal Measurements
• Great approach for characterizing reference materials! SOFTWARE
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Conclusions
• Reference materials • Can identify technical limitations/bias
• Often need multiple measurements• Orthogonal techniques
• Help to select best procedures
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Population Scale Sequencing
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Project Planning - Goals
• Submit forensic-quality whole mtGenome data to EMPOP• Current database (V3, Release 11)
• n = 26,127 control region sequences• n = 256 whole genome sequences
• NIST population samples (n > 1,000)• African American, Asian, Caucasian, Hispanic
• Sequencing plan• Start with Caucasian population• ≈ 440 mtGenomes
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Project Planning
• Questions• What instrument do we use?• What protocol/chemistry do we use?• What analysis procedure do we use?
• Software, data review, etc.
Ion Torrent S5 Ion Chef
Illumina MiSeq FGx
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Project Planning: Instrument Selection
• Considerations• Cost• Time/labor
• Automation
$-
$5,000
$10,000
$15,000
$20,000
$25,000
$30,000
S5XL AutomatedLibrary Prep
S5XL ManualLibrary Prep
MiSeq ILMNMethod
MiSeq AFDILMethod
Cost Per 96 Samples (Approximate)
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Project Planning: Protocol Selection
• Options• Illumina whole genome procedure
• Long PCR primers developed by Dr. Mark Wilson’s lab• TaKaRa LA Taq• Illumina Nextera XT library preparation• Illumina MiSeq v2 2x150 cartridge (per protocol)
• AFDIL whole genome procedure• Long PCR primers from Fendt et al., BMC Genomics 2009, 10:139• TaKaRa LA Taq (GC Buffer & BSA)• Kapa HyperPlus Library Kit• Illumina V3 2x300 cartridge
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Pilot Data – Illumina Procedure Amplification
• PCR could be more robust• 18 of 95 (≈ 18 %) of samples - low yield
• Reproducible• Only one of two amplicons affected
• Not a sample quality issue
Amplicon 1 – First try
Amplicon 1 – Second try (re-PCR)
NTC Faile
d
Faile
d
NTC
Poor
Poor
1 2 3 4 5 6 7 8 9 10 11 SS
1 2 3 4 5 6 7 8 9 10 11 SS
≈ 10 kb
≈ 10 kb
SS = Size standard
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Pilot Data – Illumina Procedure Amplification
• PCR could be more robust• 18 of 95 (≈ 18 %) of samples - low yield
• Reproducible• Amplicon 1 primer binding site mutation
• 16 of 18 low/neg samples had this • All haplogroup T (G1,888A)• HG-T frequency ≈ 10 % in Europeans
Amplicon 1 – First try
Amplicon 1 – Second try (re-PCR)
NTC Faile
d
Faile
d
NTC
Poor
Poor
1 2 3 4 5 6 7 8 9 10 11 SS
1 2 3 4 5 6 7 8 9 10 11 SS
SS = Size standard
≈ 10 kb
≈ 10 kb
AACTTTGCAAGGAGAGCCAA Primer binding site
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Library QC – Illumina Procedure
• Nextera XT library• Default parameters per protocol
• 1 ng DNA• 5 minute fragmentation
≈ 760 bp
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Sequencing Results - Illumina
• Most samples had > 99 % of mgGenome covered• Due to sensitivity of Nextera XT library prep• & Normalization of PCR input (amplicons 1 & 2 separately)
• Some gaps in coverage • Where amplification was poor
Gap areaShaded grey
Gap area
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Sequencing Results - Illumina
• Some gaps in coverage • Frequent gaps in HV2 C-stretch• Even with good overall coverage
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Pilot Data – AFDIL Procedure Amplification
• Primers from Fendt et al. 2009• TaKaRa LA Taq w/GC Buffer & BSA• 100 % of samples amplified
• Amplicon B gives higher yield than Amp A• Amp B contains control region
• Both amplicons ≈ 8 kb• Advantage of GC Buffer & BSA?
Amplicon A
Amplicon B
NTC
NTC
1 2 3 4 5 6 7 8 9 10 11 SS
1 2 3 4 5 6 7 8 9 10 11 SS
SS = Size standard
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Protocol Optimization – Kapa HyperPlus
• What are the best parameters for library preparation?• Fragmentation time
• 5 min to 30 min• Input DNA
• 10 ng to 1000 ng (PCR product)
• Optimum library size • 2 x 300 bp cartridge planned• ≈ 450 bp library molecules
• 300 bp insert + 150 bp adaptors• No more than ≈ 1500 bp poor clustering
Kapa HyperPlus Technical Data Sheet (KR1145 v3.16)
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≈ 450 bpTarget size
All reactions500 ng DNA input
10 min
20 min
30 min
Fragmentation TimeOptimization
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≈ 450 bp
All reactions10 minfragmentation
10 ng
100 ng
500 ng
DNA InputOptimization
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Optimized Conditions
• Fragmentation time = 15 minutes• DNA input ≈ 300 – 400 ng
Some residual adapter dimerTarget size450 bp
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≈ 450 bp
All reactions10 min frag.,500 ng DNA
FullRx
HalfRx
Half ReactionTrial
Reaction kinetics not equal at half volume library construction.
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Pilot Data – More Consistent Coverage DepthAFDIL method allows higher multiplexing with less likelihood of dropout sites
Illumina Whole mtGenome Method (Nextera Library Kit)
AFDIL Whole mtGenome Method (Kapa Hyper Plus Library Kit)
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Pilot Data – Haplogroup Estimation
• No surprise haplogroupsSample Missing Mutations Private Mutations Haplogroup ContinentGT38086 none T16189C H1c21 Europe (H)GT38087 none none T2b6b EuropeGT38089 none T16189C J1c8a EuropeGT38091 none C10933T A15467G V EuropeGT38092 none C198T A9327G A13801G T15670C H5e1a1 Europe (H)GT38093 none none H1o EuropeGT38094 none A11252G H65 Europe (H)GT38095 -573.1C G709A C9727T I1a1b Europe (I1a1)GT38097 none G8027A G15301A K1a1b1 EuropeGT38098 A16183C -309.1C -309.2C C16111T T152C H1b1 EuropeGT38100 none -309.1C G4655A H1 EuropeGT38106 none T2416C A8817G H2a2a EuropeGT38107 none C3388A C8788T U5a1a1 EuropeGT38108 none T4373C T15313C H1+16189 EuropeJA44327 -573.1C G16474T I2 Europe (I)JM28315 -309.1C none K2a6 EuropeJT52345 none A16138G A73G H5a1c1a EuropeJT52346 none none H5g Europe
MT97121 none T16093C G7762A J1c2 EuropeMT97122 none none T2b2b EuropeMT97123 none A16158G T1a1 Europe (T1a)MT97124 T16093C -309.1C -524.3A -524.4C K1a EuropeMT97125 none T152C U5a2d1a Europe (U5a)
Cost analysis
Scenario 1: 32 samples per sequencing runThe S5XL is actually cheaper to use with smaller number of samples (chips are less expensive).
Note: the Ion Torrent product has a maximum of 32 barcodes if using Ion Chef DL8 library prepCost inflection point at number of samples = 47 - 48 where MiSeq becomes more cost effective, with certain assumptions.
Samples/runTotal samplesRuns
3266521S5MiSeq
243939.925899.1275
S5XLCost / unitCost / project486865.526790.655
Precision ID mtDNA Whole Genome Panel (P/N A30938 $3500.00 ea)$ 36.46$ 24,244.797210805.449089.7825
DL8 Library Kit (P/N A29024 $3900.80 ea)$ 121.90$ 81,063.509613731.049981.31
540 Chef Kit (P/N A30011 $6,132.80 ea)$ 766.60$ 8,049.30
Ion 540 Chip Kit (P/N A27766 $5,048.10 ea)$ 631.02$ 13,251.42
Total$ 102,364.22
MiSeqCost / unitCost / project
Clontech LA Taq Kit (P/N RR002M, 250 units, $287.00)$ 2.87$ 3,817.10
Fragment Analyzer kits for PCR quantitation (need ~ 3 runs/sample)$ 1,200.00$ 3,600.00
Nextera XT DNA Library Preparation kit (96 samples P/N FC-131-1096 $2,787.60 ea)$ 29.04$ 19,309.94
Nextera XT Barcode Kit v2 Set A (96 indices, 384 samples, P/N FC-131-2001, $909.88 ea)$ 2.37$ 1,575.70
MiSeq Cartridge v3, 600 cycle (P/N MS-102-3003, $1407.60 ea)$ 1,407.60$ 29,559.60
Total$ 57,862.34
Two caveats:
Labor - The Ion Chef would do all the library building. This is a big advantage, but without an army of Ion Chefs it would take a long time.
We haven't tried the Precision ID whole genome procedure before. Not sure how it functions. There's a whole lot of primer pairs in there.
Scenario 2: 96 samples per sequencing run
Alternate library prep uses AB Library Builder method with Fragment library kit and two amplicon strategy
Samples/runTotal samplesRuns
4866514
MiSeqCost / unitCost / project
Clontech LA Taq Kit (P/N RR002M, 250 units, $287.00)$ 2.87$ 3,817.10
Fragment Analyzer kits for PCR quantitation (need ~ 3 runs/sample)$ 1,200.00$ 3,600.00
Nextera XT DNA Library Preparation kit (96 samples P/N FC-131-1096 $2,787.60 ea)$ 29.04$ 19,309.94
Nextera XT Barcode Kit v2 Set A (96 indices, 384 samples, P/N FC-131-2001, $909.88 ea)$ 2.37$ 1,575.70
MiSeq Cartridge v3, 600 cycle (P/N MS-102-3003, $1407.60 ea)$ 1,407.60$ 19,706.40
Total$ 48,009.14
Relative Cost To Sequence on Two Platforms
S5244872963939.92000000000056865.5210805.44000000000213731.04MiSeq244872965899.12750000000056790.65499999999889089.78249999999939981.31
Cost 2
Scenario 1: 32 samples per sequencing run
Note: the Ion Torrent product has a maximum of 32 barcodes if using Ion Chef DL8 library prep
Prices per kit updated 8-23-18
S5XL - mtGenome, Automated Library PrepCost per kit# of samples per kitCost / 96 samplesCost / 32 samples
Precision ID mtDNA Whole Genome Panel (P/N A30938)358532$ 10,755.00$ 3,585.00
DL8 Library Kit (P/N A29024)374032$ 11,220.00$ 3,740.00
Precision ID Chef & Sequencing Kit (2 runs per initialization) P/N A332085340256$ 2,002.50$ 667.50
Ion 530 Chip Kit, 4 reactions (P/N A27763)2210128$ 1,657.50$ 552.50
Total$ 25,635.00$ 8,545.00
S5XL - mtGenome, Manual Library PrepCost per kit# of samples per kitCost / 96 samplesCost / 32 samples
Precision ID mtDNA Whole Genome Panel (P/N A30938)358532$ 10,755.00$ 3,585.00
Precision ID Library Kit, 96 reactions (P/N A26435)822096$ 8,220.00$ 2,740.00
Precision ID Chef & Sequencing Kit (2 runs per initialization) P/N A332085340256$ 2,002.50$ 667.50
Ion 530 Chip Kit, 4 reactions (P/N A27763)2210128$ 1,657.50$ 552.50
Total$ 22,635.00$ 7,545.00
S5XL - Control Region, Automated Library PrepCost per kit# of samples per kitCost / 96 samplesCost / 32 samples
Precision ID mtDNA Control Region Panel (P/N A31443)107432$ 3,222.00$ 1,074.00
DL8 Library Kit (P/N A29024)374032$ 11,220.00$ 3,740.00
Precision ID Chef & Sequencing Kit (2 runs per initialization) P/N A332085340256$ 2,002.50$ 667.50
Ion 530 Chip Kit, 4 reactions (P/N A27763)2210128$ 1,657.50$ 552.50
Total$ 18,102.00$ 4,960.00
S5XL - Control Region, Manual Library PrepCost per kit# of samples per kitCost / 96 samplesCost / 32 samples
Precision ID mtDNA Control Region Panel (P/N A31443)107496$ 1,074.00$ 358.00
Precision ID Library Kit, 96 reactions (P/N A26435)822096$ 8,220.00$ 2,740.00
Precision ID Chef & Sequencing Kit (2 runs per initialization) P/N A332085340256$ 2,002.50$ 667.50
Ion 530 Chip Kit, 4 reactions (P/N A27763)2210128$ 1,657.50$ 552.50
Total$ 12,954.00$ 3,960.00
MiSeq - ILMN methodCost per kit# of samples per kitCost / 96 samplesCost / 32 samples
Clontech LA Taq Kit, (P/N RR002A, 250 units)287192$ 143.50$ 47.83
Fragment Analyzer Kit - High Molecular Weight, Standard Sensitivity, for PCR quantitation (P/N DNF-492)1250250$ 480.00$ 160.00
Fragment Analyzer Kit - NGS Fragment Analysis, High Sensitivity, for library QC (P/N DNF-474)1250500$ 240.00$ 80.00
Nextera XT DNA Library Preparation kit (96 samples P/N FC-131-1096)327096$ 3,270.00$ 1,090.00
Nextera XT Barcode Kit v2 Set A (96 indices, 384 samples, P/N FC-131-2001)1020384$ 255.00$ 85.00
MiSeq Cartridge v2, 300 cycle (P/N MS-102-2002)108048$ 2,160.00$ 720.00
Total$ 5,925.00$ 1,895.00
MiSeq - AFDIL methodCost per kit# of samples per kitCost / 96 samplesCost / 32 samples
Clontech LA Taq Kit, GC Buffer (P/N RR02AG, 250 units)143192$ 71.50$ 23.83
Applied Biosystems dNTP Mix (25 mM) (P/N N8080260)68.5192$ 34.25$ 11.42
Fragment Analyzer Kit - High Molecular Weight, Standard Sensitivity, for PCR quantitation (P/N DNF-492)1250250$ 480.00$ 160.00
Fragment Analyzer Kit - NGS Fragment Analysis, High Sensitivity, for library QC (P/N DNF-474)1250500$ 240.00$ 80.00
Kapa Biosystems HyperPlus Library Kit (PCR Free), 96 reactions (P/N KK8515)297696$ 2,976.00$ 992.00
Kapa Biosystems Dual Indexed Adapter Kit, 15 uM, 20 uL each (P/N KK8722)2304384$ 576.00$ 192.00
MiSeq Cartridge v3, 600 cycle (P/N MS-102-3003)158096$ 1,580.00$ 526.67
Total$ 5,372.00$ 1,710.67
Cost graph
Cost Per 96 Samples (Approximate)
S5XL Automated Library Prep$ 25,635
S5XL Manual Library Prep$ 12,954
MiSeq ILMN Method$ 5,925
MiSeq AFDIL Method$ 5,372
Cost Per 96 Samples (Approximate)S5XL Automated Library PrepS5XL Manual Library PrepMiSeq ILMN MethodMiSeq AFDIL Method256351295459255372
Gantt Chart
TaskDec 2017Jan 2018Feb 2018Mar 2018Apr 2018May 2018Jun 2018Jul 2018Aug 2018Sept 2018Oct 2018Nov 2018Dec 2018
Procure reagents
PCR Cauc 1
Library prep
Sequence
PCR Cauc 2
Library prep
Sequence
PCR Comb 1/2
Library prep
Sequence
PCR Cauc "Other", reruns
Library prep
Sequence
Data Analysis
Cauc 1 Variants, haplogroups
Cauc 2 Variants, haplogroups
Comb 1/2 Variants, haplogroups
Cauc "Other" Variants, haplogroups
Write Up
Data QC
Submit to EMPOP
Manuscript writing
Revisions
Submit to Journal
Budget
Caucasian samples (n = 440)Reactions = 480
Reagent namePart #CostNumber of samples / kitKits neededTotal costAlready have?More neededRemaining cost
Takara LA Taq with GC Buffer (125 unit)RR02AG$ 143.009610$ 1,430.0064$ 572.00
GeneAmp dNTP Blend (2.5 mM ea), ThermoFisherN8080260$ 68.5019210$ 685.0064$ 274.00
AATI High MW Fragment Analysis KitDNF-492$ 2,500.005002$ 5,000.0011$ 2,500.00
Kapa Hyper Prep (without amplification)KK8505$ 2,400.00965$ 12,000.0014$ 9,600.00
KAPA Pure BeadsKK8002$ 720.002502$ 1,440.0011$ 720.00
KAPA Dual-Indexed Adapter KitKK8722$ 2,304.003002$ 4,608.0011$ 2,304.00
AATI High Sensitivity NGS Fragment Analysis KitDNF-474$ 2,500.005001$ 2,500.0001$ 2,500.00
MiSeq V3 Reagent Kit (600 cycle)MS-102-3003$ 1,580.00965$ 7,900.0023$ 4,740.00
Total cost$ 35,563.00Remaining cost$ 23,210.00
Platemaps
C1GT38095JM28315MT97126MT97155TT51677UT58305GT38072GT36864JT51178MT94827MT9484295
GT38086GT38097JT52345MT97131MT97156TT51679UT58310GT38073GT36866JT51211MT94829MT94843
GT38087GT38098JT52346MT97136MT97158TT51680ZT81382GT38075GT36875MT94803MT94831MT94846
GT38089GT38100MT97121MT97139MT97159TT51682GT38065GT38076GT36877MT94807MT94833MT94848
GT38091GT38106MT97122MT97141PT86478TT51683GT38066GT38078GT36878MT94815MT94834MT94850
GT38092GT38107MT97123MT97145TT51669TT51684GT38067GT38081GT36884MT94817MT94835MT94853
GT38093GT38108MT97124MT97150TT51675TT51685GT38069GT38083GT36885MT94818MT94838MT94855
GT38094JA44327MT97125MT97152TT51676UT58303GT38070GC03394GT36886MT94826MT94839MT94858
C2MT97185MT97199TT51702WT52470WT52486ZT81380MT97167UA16894UA16921UT58298UT5831895
MT97173MT97186MT97200TT51703WT52471WT52490ZT81381OT07753UA16895UA16924UT58299UT58319
MT97176MT97187OT07803UT58333WT52472WT52493GT38114OT07760UA16896UA16927UT58300UT58320
MT97177MT97188TT51689UT58334WT52474ZC08844GT38119OT07767UA16897UA16928UT58301UT58321
MT97178MT97189TT51693UT58335WT52477ZT81337MT97163OT07776UA16899UA16929UT58302UT58324
MT97179MT97192TT51694UT58336WT52480ZT81342MT97164OT07785UA16903UC10177UT58314WA29566
MT97180MT97195TT51696UT58337WT52482ZT81372MT97165PT86536UA16908UC10178UT58315WA29572
MT97184MT97196TT51698WT52457WT52485ZT81377MT97166UA16891UA16918UT58295UT58317WA29583
CMB1UT57318WT51362WA29594JT51471OT05897PT84223PT84232GT37778GT37900TT51422ZT8078631
UT57300WT51342WT51373WA29612JT51499OT05898PT84224PT84234GT37812GT37913TT51435ZT80815
UT57301WT51343WT51378ZT81387OT05888OT05899PT84225PT84236GT37828JT52076TT51483ZT80826
UT57302WT51345WT51381MT94859OT05890OT05901PT84226PT84239ZT80932OT07280TT51511ZT80863
UT57303WT51354WT51386MT94866OT05892PT84214PT84227PT84240GT37862PT85612TT51530ZT80865
UT57310WT51355BC11352MT94868OT05893PT84215PT84228PT84241GT37864PT85658ZT80731ZT80869
UT57312WT51358MT97172MT94869OT05894PT84216PT84230PT84242GT37869TT51399ZT80737ZT80870
UT57317WT51359WA29584MT94875OT05896PT84222PT84231PT84243GT37888TT51407ZT80782ZT80925
CMB2MT94892TT50701UT57287PT84244ZT79619PT84212ZT79617Y6Y15Y23Y3141
MT94877MT94893TT50705UT57288PT84245PT84201PT84213ZT79618Y7Y16Y24Y32
MT94880PT83505TT50708UT57292PT84247PT84202PT84248GT37853Y8Y17Y25Y33
MT94882PT83535TT50720UT57293PT84256PT84206PT84249Y1Y9Y18Y26Y34
MT94883PT83538TT50721UT57299TT50913PT84208PT84251Y2Y10Y19Y27Y35
MT94884TT50697UT57281UT57635TT50916PT84209PT84252Y3Y12Y20Y28Y36
MT94886TT50698UT57283OT06795TT50922PT84210PT84253Y4Y13Y21Y29Y37
MT94888TT50700UT57286PC16856TT50923PT84211PT84254Y5Y14Y22Y30Y38262Should be 263
123456789101112
ABlankAF08CAF16CAF24CAF32CAF40CAF48CAF56CAF64CAF72CAF80CAF88C
BAF01CAF09CAF17CAF25CAF33CAF41CAF49CAF57CAF65CAF73CAF81CAF89C
CAF02CAF10CAF18CAF26CAF34CAF42CAF50CAF58CAF66CAF74CAF82CAF90C
DAF03CAF11CAF19CAF27CAF35CAF43CAF51CAF59CAF67CAF75CAF83CAF91C
EAF04CAF12CAF20CAF28CAF36CAF44CAF52CAF60CAF68CAF76CAF84CAF92C
FAF05CAF13CAF21CAF29CAF37CAF45CAF53CAF61CAF69CAF77CAF85CAF93C
GAF06CAF14CAF22CAF30CAF38CAF46CAF54CAF62CAF70CAF78CAF86CAF94CCaucasian Fathers
HAF07CAF15CAF23CAF31CAF39CAF47CAF55CAF63CAF71CAF79CAF87CAF95C90
123456789101112
ABlankC08CC16CC24CC32CC40CC48CC56CC64CC72CC80CC88C
BC01CC09CC17CC25CC33CC41CC49CC57CC65CC73CC81CC89C
CC02CC10CC18CC26CC34CC42CC50CC58CC66CC74CC82CC90C
DC03CC11CC19CC27CC35CC43CC51CC59CC67CC75CC83CC91C
EC04CC12CC20CC28CC36CC44CC52CC60CC68CC76CC84CC92C
FC05CC13CC21CC29CC37CC45CC53CC61CC69CC77CC85CC93C
GC06CC14CC22CC30CC38CC46CC54CC62CC70CC78CC86CC94CCaucasian Sons
HC07CC15CC23CC31CC39CC47CC55CC63CC71CC79CC87CC95C80
123456789101112
A
BAF96BAF96AAF96CAF96HC96BC96AC96CC96H
CAF97BAF97AAF97CAF97HC97BC97AC97CC97H
DAF98BAF98AAF98CAF98HC98BC98AC98CC98H
EAF99BAF99AAF99CAF99HC99BC99AC99CC99HAdditional Caucasian
FAF100BAF100AAF100CAF100HC100BC100AC100CC100H8
GAF101AC101A
H
Af AmerAsianCaucHispAf AmerAsianCaucHisp
FathersSonsTotal Caucasian mitogenomes
262 + 178 = 440
Progress - Fendt
PlateWellPopulationSample NameQuant Amp A (ng/uL)Quant Amp B (ng/uL)Amount of Amp1Amount of Amp2Total (ng)Use 1/2Library Conc (nmol/L)
C1A01CaucNTCPCR 4-2-18No ampNTC102ERROR:#VALUE!ERROR:#VALUE!
C1A02CaucGT38095PCR 4-2-1867.49191.341021057.5598528.7799165.042018/6/11 Use 10 uL of Amp A, 2 uL of Amp B in total volume of 100 uL.
C1A03CaucJM28315PCR 4-2-1861.60287.211021190.4286595.2143161.528Average concentration is 10 ng/uL (~600 ng Amp A, 500 ng Amp B) for C1 plate.
C1A04CaucMT97126PCR 4-2-1873.07214.361021159.4288579.7144143.005Use 35 uL in Frag Rx.
C1A05CaucMT97155PCR 4-2-1884.61214.561021275.229637.6145193.669Substitute 2392 A for A08 (GT38072) and 2392 B for A09 (GT36864), used for frag opt.
C1A06CaucTT51677PCR 4-2-1894.20241.181021424.369712.1845145.559
C1A07CaucUT58305PCR 4-2-1841.12192.10102795.3452397.6726127.02
C1A08CaucGT38072PCR 4-2-18124.51255.661021756.4354878.217799.813WellSample IDPeak IDSize (bp)ng/ulUse PCRH2O
C1A09CaucGT36864PCR 4-2-18104.59273.591021593.0238796.5119153.926A1SampA16885389.47392392 AFendt A5.673.7
C1A10CaucJT51178PCR 4-2-1825.21167.41102586.8896293.444877.133A2SampA26876572.82382392 BFendt A6.981.0
C1A11CaucMT94827PCR 4-2-1828.28191.60102665.9738332.9869147.072A5SampA53933824.13842392 AFendt B20.7
C1A12CaucMT94842PCR 4-2-1819.67267.63102731.9532365.9766247.448A6SampA63894241.14232392 BFendt B12.2
C1B01CaucGT38086PCR 4-2-1869.70286.771021270.5776635.2888105.214
C1B02CaucGT38097PCR 4-2-1869.27276.671021246.0026623.0013191.778
C1B03CaucJT52345PCR 4-2-1855.06234.201021018.9648509.4824125.385
C1B04CaucMT97131PCR 4-2-1860.99217.811021045.5468522.7734150.042018/06/12 based on average of 170 nM library concentration:
C1B05CaucMT97156PCR 4-2-1849.06181.24102853.0652426.5326168.23Pool all 96 libraries
C1B06CaucTT51679PCR 4-2-1859.14243.631021078.7084539.3542153.954Dilute to 4 nM, follow ILMN denature and dilute guide.
C1B07CaucUT58310PCR 4-2-1821.36186.27102586.1442293.0721131.7Initial concFinal ConcFinal VolInitial library VolPlus Diluent
C1B08CaucGT38073PCR 4-2-1867.14232.111021135.576567.788209.35617042004.71195.29
C1B09CaucGT36866PCR 4-2-1882.75267.401021362.2578681.1289272.39
C1B10CaucJT51211PCR 4-2-1868.11203.571021088.2846544.1423153.786
C1B11CaucMT94829PCR 4-2-1830.57168.87102643.4624321.7312149.269
C1B12CaucMT94843PCR 4-2-1812.00169.02102458.0152229.0076133.957
C1C01CaucGT38087PCR 4-2-1866.20288.911021239.8766619.938380.684
C1C02CaucGT38098PCR 4-2-1857.82264.221021106.666553.333148.421
C1C03CaucJT52346PCR 4-2-1865.52258.231021171.6316585.8158125.232
C1C04CaucMT97136PCR 4-2-1861.94285.421021190.234595.117146.537
C1C05CaucMT97158PCR 4-2-1861.74281.871021181.1798590.5899159.405
C1C06CaucTT51680PCR 4-2-1859.07223.251021037.2294518.6147125.865
C1C07CaucZT81382PCR 4-2-1865.51265.111021185.369592.6845189.598
C1C08CaucGT38075PCR 4-2-1887.82283.011021444.2656722.1328213.813
C1C09CaucGT36875PCR 4-2-1892.39255.441021434.7416717.3708223.184
C1C10CaucMT94803PCR 4-2-1828.92217.52102724.287362.143590.004
C1C11CaucMT94831PCR 4-2-1855.23219.71102991.7334495.8667187.873
C1C12CaucMT94846PCR 4-2-1833.59276.29102888.4346444.2173253.346
C1D01CaucGT38089PCR 4-2-1866.34285.641021234.6498617.324994.631
C1D02CaucGT38100PCR 4-2-1875.13294.381021340.0998670.0499189.04
C1D03CaucMT97121PCR 4-2-1878.33195.471021174.1902587.0951157.048
C1D04CaucMT97139PCR 4-2-1848.30304.421021091.8476545.9238147.929
C1D05CaucMT97159PCR 4-2-1844.96188.87102827.369413.6845153.287
C1D06CaucTT51682PCR 4-2-1899.57298.861021593.4514796.7257250.823
C1D07CaucGT38065PCR 4-2-1884.80219.921021287.8198643.9099239.535
C1D08CaucGT38076PCR 4-2-1871.91253.211021225.5036612.7518238.511
C1D09CaucGT36877PCR 4-2-1895.62280.561021517.3314758.6657289.015
C1D10CaucMT94807PCR 4-2-18109.89284.301021667.5136833.7568242.782
C1D11CaucMT94833PCR 4-2-1819.61170.65102537.3644268.6822
C1D12CaucMT94848PCR 4-2-1825.90285.48102829.933414.9665212.181
C1E01CaucGT38091PCR 4-2-1884.51356.811021558.7192779.359686.897
C1E02CaucGT38106PCR 4-2-1867.65291.761021260.0044630.0022170.874
C1E03CaucMT97122PCR 4-2-1855.14336.631021224.6842612.3421117.7
C1E04CaucMT97141PCR 4-2-1862.49327.461021279.8442639.9221153.259
C1E05CaucPT86478PCR 4-2-1850.39223.32102950.5654475.2827138.508
C1E06CaucTT51683PCR 4-2-1864.90241.461021131.8958565.9479151.047
C1E07CaucGT38066PCR 4-2-1892.53326.561021578.4664789.2332239.912
C1E08CaucGT38078PCR 4-2-1882.05290.711021401.9124700.9562200.925
C1E09CaucGT36878PCR 4-2-1896.34233.351021430.0748715.0374200.483
C1E10CaucMT94815PCR 4-2-1889.09318.711021528.3052764.1526190.944
C1E11CaucMT94834PCR 4-2-1863.60288.521021213.0878606.5439221.239
C1E12CaucMT94850PCR 4-2-1822.81284.85102797.752398.876230.406
C1F01CaucGT38092PCR 4-2-1849.36268.621021030.8226515.411363.938
C1F02CaucGT38107PCR 4-2-1870.28237.121021177.0086588.5043175.192
C1F03CaucMT97123PCR 4-2-1858.57232.061021049.829524.9145117.907
C1F04CaucMT97145PCR 4-2-1861.16294.251021200.1258600.0629146.126
C1F05CaucTT51669PCR 4-2-1841.67254.03102924.7366462.3683126.545
C1F06CaucTT51684PCR 4-2-1855.65226.461021009.4272504.7136146.724
C1F07CaucGT38067PCR 4-2-1879.13238.311021267.8842633.9421213.167
C1F08CaucGT38081PCR 4-2-1870.72242.121021191.404595.702205.687
C1F09CaucGT36884PCR 4-2-1876.29304.621021372.1154686.0577220.416
C1F10CaucMT94817PCR 4-2-1888.93283.771021456.8618728.4309204.126
C1F11CaucMT94835PCR 4-2-1850.75191.34102890.2068445.1034192.665
C1F12CaucMT94853PCR 4-2-180.57283.92102573.5094286.7547223.42
C1G01CaucGT38093PCR 4-2-1895.35280.891021515.2748757.6374106.875
C1G02CaucGT38108PCR 4-2-1832.21228.14102778.3722389.1861107.631
C1G03CaucMT97124PCR 4-2-1877.07235.401021241.4802620.7401156.672
C1G04CaucMT97150PCR 4-2-1859.66242.461021081.569540.7845139.678
C1G05CaucTT51675PCR 4-2-1843.06238.10102906.772453.386
C1G06CaucTT51685PCR 4-2-1859.66227.821021052.2914526.1457163.171
C1G07CaucGT38069PCR 4-2-18103.26353.021021738.6692869.3346288.833
C1G08CaucGT38083PCR 4-2-1858.60217.071021020.1914510.0957169.224
C1G09CaucGT36885PCR 4-2-1890.16255.461021412.4738706.2369279.958
C1G10CaucMT94818PCR 4-2-1895.22299.931021552.0812776.0406244.366
C1G11CaucMT94838PCR 4-2-180.245.2110212.78846.3942Size of B amplicon not consistent2.056
C1G12CaucMT94855PCR 4-2-1835.59293.19102942.282471.141291.885
C1H01CaucGT38094PCR 4-2-1826.80231.20102730.4192365.209671.427
C1H02CaucJA44327PCR 4-2-1832.27214.91102752.5162376.2581178.969
C1H03CaucMT97125PCR 4-2-1831.44247.42102809.2154404.6077157.39
C1H04CaucMT97152PCR 4-2-1829.58217.10102730.0258365.0129149.256
C1H05CaucTT51676PCR 4-2-1835.30155.40102663.8068331.9034132.289
C1H06CaucUT58303PCR 4-2-1836.43188.56102741.4458370.7229129.69
C1H07CaucGT38070PCR 4-2-1844.88265.85102980.5456490.2728261.257
C1H08CaucGC03394PCR 4-2-1836.30234.86102832.6916416.3458217.587
C1H09CaucGT36886PCR 4-2-1832.38185.79102695.335347.6675192.389
C1H10CaucMT94826PCR 4-2-1816.64231.74102629.831314.9155170.251
C1H11CaucMT94839PCR 4-2-180.34241.09102485.5516242.7758188.405
C1H12CaucMT94858PCR 4-2-1862.85281.111021190.7072595.3536155.469
Average58.90247.300.2381711494Average1083.60170.5Average
Min0.245.21291.9Max
Max124.51356.812.1Min
Quant Amp A (ng/uL)Quant Amp B (ng/uL)
NTC2018-08-20 Combine AmpA/AmpB in 1:3 ratio (average is 27ng & 9 ng/ul)
C2A02CaucMT97185PCR 8-10-1817.363.83Mix 5 ul Amp A + 15 ul Amp B --> ((5*27)+(15*9)/20) = 13.5 ng/ul
C2A03CaucMT97199PCR 8-10-1827.5211.46Use 17.5 uL in Frag Rx. (Note this will be below desired 350 ng input (@ ~ 235 ng).)
C2A04CaucTT51702PCR 8-10-1814.973.20Run SRM 2391d components A-E (PCR 8/8/2018)
C2A05CaucWT52470PCR 8-10-1829.3913.15
C2A06CaucWT52486PCR 8-10-1824.1012.82
C2A07CaucZT81380PCR 8-10-1830.489.32WellSample IDPeak IDSize (bp)ng/ulUse PCRH2O
C2A08CaucMT97167PCR 8-10-1818.554.45
C2A09CaucUA16894PCR 8-10-1833.006.89
C2A10CaucUA16921PCR 8-10-1833.638.97
C2A11CaucUT58298PCR 8-10-1846.439.96
C2A12CaucUT58318PCR 8-10-1826.544.52
C2B01CaucMT97173PCR 8-10-1826.709.74
C2B02CaucMT97186PCR 8-10-1829.829.61
C2B03CaucMT97200PCR 8-10-1821.278.96
C2B04CaucTT51703PCR 8-10-1820.208.39
C2B05CaucWT52471PCR 8-10-1825.9915.67
C2B06CaucWT52490PCR 8-10-1819.8610.19
C2B07CaucZT81381PCR 8-10-189.661.31
C2B08CaucOT07753PCR 8-10-1826.9810.16
C2B09CaucUA16895PCR 8-10-1831.075.362018/06/12 based on average of 170 nM library concentration:
C2B10CaucUA16924PCR 8-10-1821.1510.49Pool all 96 libraries
C2B11CaucUT58299PCR 8-10-1841.289.90Dilute to 4 nM, follow ILMN denature and dilute guide.
C2B12CaucUT58319PCR 8-10-1835.2013.20Initial concFinal ConcFinal VolInitial library VolPlus Diluent
C2C01CaucMT97176PCR 8-10-1826.246.7817042004.71195.29
C2C02CaucMT97187PCR 8-10-1827.3811.74
C2C03CaucOT07803PCR 8-10-1822.403.42
C2C04CaucUT58333PCR 8-10-1815.465.28
C2C05CaucWT52472PCR 8-10-1818.514.86
C2C06CaucWT52493PCR 8-10-1820.176.59
C2C07CaucGT38114PCR 8-10-1821.2111.46
C2C08CaucOT07760PCR 8-10-1834.6015.05
C2C09CaucUA16896PCR 8-10-1825.526.74
C2C10CaucUA16927PCR 8-10-1823.447.92
C2C11CaucUT58300PCR 8-10-1834.2212.75
C2C12CaucUT58320PCR 8-10-1825.517.52
C2D01CaucMT97177PCR 8-10-1826.057.17
C2D02CaucMT97188PCR 8-10-1834.327.59
C2D03CaucTT51689PCR 8-10-1826.9610.85
C2D04CaucUT58334PCR 8-10-1822.377.76
C2D05CaucWT52474PCR 8-10-1819.116.92
C2D06CaucZC08844PCR 8-10-1846.0615.87
C2D07CaucGT38119PCR 8-10-1842.7919.08
C2D08CaucOT07767PCR 8-10-1827.564.68
C2D09CaucUA16897PCR 8-10-1823.237.63
C2D10CaucUA16928PCR 8-10-1823.817.12
C2D11CaucUT58301PCR 8-10-1845.9612.28
C2D12CaucUT58321PCR 8-10-1835.3110.08
C2E01CaucMT97178PCR 8-10-1831.478.95
C2E02CaucMT97189PCR 8-10-1827.2613.11
C2E03CaucTT51693PCR 8-10-1817.765.87
C2E04CaucUT58335PCR 8-10-1821.424.01
C2E05CaucWT52477PCR 8-10-1821.566.86
C2E06CaucZT81337PCR 8-10-1834.4411.99
C2E07CaucMT97163PCR 8-10-1836.5111.84
C2E08CaucOT07776PCR 8-10-1821.446.61
C2E09CaucUA16899PCR 8-10-1823.894.85
C2E10CaucUA16929PCR 8-10-1830.135.52
C2E11CaucUT58302PCR 8-10-1833.3514.29
C2E12CaucUT58324PCR 8-10-1832.799.29
C2F01CaucMT97179PCR 8-10-1825.369.76
C2F02CaucMT97192PCR 8-10-1819.224.64
C2F03CaucTT51694PCR 8-10-1822.308.04
C2F04CaucUT58336PCR 8-10-1818.965.01
C2F05CaucWT52480PCR 8-10-1829.1212.16
C2F06CaucZT81342PCR 8-10-1833.839.98
C2F07CaucMT97164PCR 8-10-1833.1115.22
C2F08CaucOT07785PCR 8-10-1823.578.18
C2F09CaucUA16903PCR 8-10-1814.944.52
C2F10CaucUC10177PCR 8-10-1828.8011.65
C2F11CaucUT58314PCR 8-10-1827.528.48
C2F12CaucWA29566PCR 8-10-1846.4615.16
C2G01CaucMT97180PCR 8-10-1819.368.16
C2G02CaucMT97195PCR 8-10-1825.403.60
C2G03CaucTT51696PCR 8-10-1828.358.85
C2G04CaucUT58337PCR 8-10-1818.007.60
C2G05CaucWT52482PCR 8-10-1815.606.08
C2G06CaucZT81372PCR 8-10-1821.673.53
C2G07CaucMT97165PCR 8-10-1822.316.79
C2G08CaucPT86536PCR 8-10-1822.634.42
C2G09CaucUA16908PCR 8-10-1815.036.24
C2G10CaucUC10178PCR 8-10-1824.148.96
C2G11CaucUT58315PCR 8-10-1833.7311.47
C2G12CaucWA29572PCR 8-10-1823.429.49
C2H01CaucMT97184PCR 8-10-1821.365.05
C2H02CaucMT97196PCR 8-10-1825.689.58
C2H03CaucTT51698PCR 8-10-1823.477.43
C2H04CaucWT52457PCR 8-10-1839.979.28
C2H05CaucWT52485PCR 8-10-1822.6213.65
C2H06CaucZT81377PCR 8-10-1825.134.77
C2H07CaucMT97166PCR 8-10-1839.519.13
C2H08CaucUA16891PCR 8-10-1819.464.20
C2H09CaucUA16918PCR 8-10-1832.478.76
C2H10CaucUT58295PCR 8-10-1838.8418.29
C2H11CaucUT58317PCR 8-10-1826.535.90
C2H12CaucWA29583PCR 8-10-1819.707.78
Average26.738.67
Min9.661.31
Max46.4619.08
Combo1A02CaucUT57318
Combo1A03CaucWT51362
Combo1A04CaucWA29594
Combo1A05AAJT51471
Combo1A06AAOT05897
Combo1A07AAPT84223
Combo1A08AAPT84232
Combo1A09HispGT37778
Combo1A10HispGT37900
Combo1A11HispTT51422
Combo1A12HispZT80786
Combo1B01CaucUT57300
Combo1B02CaucWT51342
Combo1B03CaucWT51373
Combo1B04CaucWA29612
Combo1B05AAJT51499
Combo1B06AAOT05898
Combo1B07AAPT84224
Combo1B08AAPT84234
Combo1B09HispGT37812
Combo1B10HispGT37913
Combo1B11HispTT51435
Combo1B12HispZT80815
Combo1C01CaucUT57301
Combo1C02CaucWT51343
Combo1C03CaucWT51378
Combo1C04CaucZT81387
Combo1C05AAOT05888
Combo1C06AAOT05899
Combo1C07AAPT84225
Combo1C08AAPT84236
Combo1C09HispGT37828
Combo1C10HispJT52076
Combo1C11HispTT51483
Combo1C12HispZT80826
Combo1D01CaucUT57302
Combo1D02CaucWT51345
Combo1D03CaucWT51381
Combo1D04CaucMT94859
Combo1D05AAOT05890
Combo1D06AAOT05901
Combo1D07AAPT84226
Combo1D08AAPT84239
Combo1D09HispZT80932
Combo1D10HispOT07280
Combo1D11HispTT51511
Combo1D12HispZT80863
Combo1E01CaucUT57303
Combo1E02CaucWT51354
Combo1E03CaucWT51386
Combo1E04CaucMT94866
Combo1E05AAOT05892
Combo1E06AAPT84214
Combo1E07AAPT84227
Combo1E08AAPT84240
Combo1E09HispGT37862
Combo1E10HispPT85612
Combo1E11HispTT51530
Combo1E12HispZT80865
Combo1F01CaucUT57310
Combo1F02CaucWT51355
Combo1F03CaucBC11352
Combo1F04CaucMT94868
Combo1F05AAOT05893
Combo1F06AAPT84215
Combo1F07AAPT84228
Combo1F08AAPT84241
Combo1F09HispGT37864
Combo1F10HispPT85658
Combo1F11HispZT80731
Combo1F12HispZT80869
Combo1G01CaucUT57312
Combo1G02CaucWT51358
Combo1G03CaucMT97172
Combo1G04CaucMT94869
Combo1G05AAOT05894
Combo1G06AAPT84216
Combo1G07AAPT84230
Combo1G08AAPT84242
Combo1G09HispGT37869
Combo1G10HispTT51399
Combo1G11HispZT80737
Combo1G12HispZT80870
Combo1H01CaucUT57317
Combo1H02CaucWT51359
Combo1H03CaucWA29584
Combo1H04CaucMT94875
Combo1H05AAOT05896
Combo1H06AAPT84222
Combo1H07AAPT84231
Combo1H08AAPT84243
Combo1H09HispGT37888
Combo1H10HispTT51407
Combo1H11HispZT80782
Combo1H12HispZT80925
Combo2A02CaucMT94892
Combo2A03CaucTT50701
Combo2A04CaucUT57287
Combo2A05AAPT84244
Combo2A06AAZT79619
Combo2A07AAPT84212
Combo2A08AAZT79617
Combo2A09CaucY6
Combo2A10AAY15
Combo2A11HispY23
Combo2A12CaucY31
Combo2B01CaucMT94877
Combo2B02CaucMT94893
Combo2B03CaucTT50705
Combo2B04CaucUT57288
Combo2B05AAPT84245
Combo2B06AAPT84201
Combo2B07AAPT84213
Combo2B08AAZT79618
Combo2B09CaucY7
Combo2B10AAY16
Combo2B11HispY24
Combo2B12CaucY32
Combo2C01CaucMT94880
Combo2C02CaucPT83505
Combo2C03CaucTT50708
Combo2C04CaucUT57292
Combo2C05AAPT84247
Combo2C06AAPT84202
Combo2C07AAPT84248
Combo2C08HispGT37853
Combo2C09CaucY8
Combo2C10AAY17
Combo2C11HispY25
Combo2C12AAY33
Combo2D01CaucMT94882
Combo2D02CaucPT83535
Combo2D03CaucTT50720
Combo2D04CaucUT57293
Combo2D05AAPT84256
Combo2D06AAPT84206
Combo2D07AAPT84249
Combo2D08CaucY1
Combo2D09CaucY9
Combo2D10AAY18
Combo2D11HispY26
Combo2D12AAY34
Combo2E01CaucMT94883
Combo2E02CaucPT83538
Combo2E03CaucTT50721
Combo2E04CaucUT57299
Combo2E05AATT50913
Combo2E06AAPT84208
Combo2E07AAPT84251
Combo2E08CaucY2
Combo2E09CaucY10
Combo2E10AAY19
Combo2E11HispY27
Combo2E12AAY35
Combo2F01CaucMT94884
Combo2F02CaucTT50697
Combo2F03CaucUT57281
Combo2F04AsianUT57635
Combo2F05AATT50916
Combo2F06AAPT84209
Combo2F07AAPT84252
Combo2F08CaucY3
Combo2F09CaucY12
Combo2F10HispY20
Combo2F11HispY28
Combo2F12AAY36
Combo2G01CaucMT94886
Combo2G02CaucTT50698
Combo2G03CaucUT57283
Combo2G04AsianOT06795
Combo2G05AATT50922
Combo2G06AAPT84210
Combo2G07AAPT84253
Combo2G08CaucY4
Combo2G09AAY13
Combo2G10HispY21
Combo2G11HispY29
Combo2G12AAY37
Combo2H01CaucMT94888
Combo2H02CaucTT50700
Combo2H03CaucUT57286
Combo2H04AsianPC16856
Combo2H05AATT50923
Combo2H06AAPT84211
Combo2H07AAPT84254
Combo2H08CaucY5
Combo2H09AAY14
Combo2H10HispY22
Combo2H11HispY30
Combo2H12HispY38
BlankPCR 2018-08-08
AF01CPCR 2018-08-08Failed to amplify
AF02CPCR 2018-08-08Failed to amplify
AF03CPCR 2018-08-08Failed to amplify
AF04CPCR 2018-08-08Failed to amplify
AF05CPCR 2018-08-08Failed to amplify
AF06CPCR 2018-08-08Failed to amplify
AF07CPCR 2018-08-08Failed to amplify
AF08CPCR 2018-08-08Failed to amplify
AF09CPCR 2018-08-08Failed to amplify
AF10CPCR 2018-08-08Failed to amplify
AF11CPCR 2018-08-08Failed to amplify
AF12CPCR 2018-08-08Failed to amplify
AF13CPCR 2018-08-08Failed to amplify
AF14CPCR 2018-08-08Failed to amplify
AF15CPCR 2018-08-08Failed to amplify
AF16CPCR 2018-08-08Failed to amplify
AF17CPCR 2018-08-08Failed to amplify
AF18CPCR 2018-08-08Failed to amplify
AF19CPCR 2018-08-08Failed to amplify
AF20CPCR 2018-08-08Failed to amplify
AF21CPCR 2018-08-08Failed to amplify
AF22CPCR 2018-08-08Failed to amplify
AF23CPCR 2018-08-08Failed to amplify
AF24CPCR 2018-08-08Failed to amplify
AF25CPCR 2018-08-08Failed to amplify
AF26CPCR 2018-08-08Failed to amplify
AF27CPCR 2018-08-08Failed to amplify
AF28CPCR 2018-08-08Failed to amplify
AF29CPCR 2018-08-08Failed to amplify
AF30CPCR 2018-08-08Failed to amplify
AF31CPCR 2018-08-08Failed to amplify
AF32CPCR 2018-08-08Failed to amplify
AF33CPCR 2018-08-08Failed to amplify
AF34CPCR 2018-08-08Failed to amplify
AF35CPCR 2018-08-08Failed to amplify
AF36CPCR 2018-08-08Failed to amplify
AF37CPCR 2018-08-08Failed to amplify
AF38CPCR 2018-08-08Failed to amplify
AF39CPCR 2018-08-08Failed to amplify
AF40CPCR 2018-08-08Failed to amplify
AF41CPCR 2018-08-08Failed to amplify
AF42CPCR 2018-08-08Failed to amplify
AF43C
AF44C
AF45C
AF46C
AF47C
AF48C
AF49C
AF50C
AF51C
AF52C
AF53C
AF54C
AF55C
AF56C
AF57C
AF58C
AF59C
AF60C
AF61C
AF62C
AF63C
AF64C
AF65C
AF66C
AF67C
AF68C
AF69C
AF70C
AF71C
AF72C
AF73C
AF74C
AF75C
AF76C
AF77C
AF78C
AF79C
AF80C
AF81C
AF82C
AF83C
AF84C
AF85C
AF86C
AF87C
AF88C
AF89C
AF90C
AF91C
AF92C
AF93C
AF94C
AF95C
Samplesheets
A1Empty_A1
C1GT38095JM28315MT97126MT97155TT51677UT58305GT38072GT36864JT51178MT94827MT9484295C1A02CaucGT38095A2Empty_A2
GT38086GT38097JT52345MT97131MT97156TT51679UT58310GT38073GT36866JT51211MT94829MT94843C1A03CaucJM28315A3Empty_A3
GT38087GT38098JT52346MT97136MT97158TT51680ZT81382GT38075GT36875MT94803MT94831MT94846C1A04CaucMT97126A4Empty_A4
GT38089GT38100MT97121MT97139MT97159TT51682GT38065GT38076GT36877MT94807MT94833MT94848C1A05CaucMT97155A5Empty_A5
GT38091GT38106MT97122MT97141PT86478TT51683GT38066GT38078GT36878MT94815MT94834MT94850C1A06CaucTT51677A6Empty_A6
GT38092GT38107MT97123MT97145TT51669TT51684GT38067GT38081GT36884MT94817MT94835MT94853C1A07CaucUT58305A7Empty_A7
GT38093GT38108MT97124MT97150TT51675TT51685GT38069GT38083GT36885MT94818MT94838MT94855C1A08CaucGT38072A8Empty_A8
GT38094JA44327MT97125MT97152TT51676UT58303GT38070GC03394GT36886MT94826MT94839MT94858C1A09CaucGT36864A9Empty_A9
C1A10CaucJT51178A10Empty_A10
C2MT97185MT97199TT51702WT52470WT52486ZT81380MT97167UA16894UA16921UT58298UT5831895C1A11CaucMT94827A11Empty_A11
MT97173MT97186MT97200TT51703WT52471WT52490ZT81381OT07753UA16895UA16924UT58299UT58319C1A12CaucMT94842A12Empty_A12
MT97176MT97187OT07803UT58333WT52472WT52493GT38114OT07760UA16896UA16927UT58300UT58320C1B01CaucGT38086B1Empty_B1
MT97177MT97188TT51689UT58334WT52474ZC08844GT38119OT07767UA16897UA16928UT58301UT58321C1B02CaucGT38097B2Empty_B2
MT97178MT97189TT51693UT58335WT52477ZT81337MT97163OT07776UA16899UA16929UT58302UT58324C1B03CaucJT52345B3Empty_B3
MT97179MT97192TT51694UT58336WT52480ZT81342MT97164OT07785UA16903UC10177UT58314WA29566C1B04CaucMT97131B4Empty_B4
MT97180MT97195TT51696UT58337WT52482ZT81372MT97165PT86536UA16908UC10178UT58315WA29572C1B05CaucMT97156B5Empty_B5
MT97184MT97196TT51698WT52457WT52485ZT81377MT97166UA16891UA16918UT58295UT58317WA29583C1B06CaucTT51679B6Empty_B6
C1B07CaucUT58310B7Empty_B7
CMB1UT57318WT51362WA29594JT51471OT05897PT84223PT84232GT37778GT37900TT51422ZT8078631C1B08CaucGT38073B8Empty_B8
UT57300WT51342WT51373WA29612JT51499OT05898PT84224PT84234GT37812GT37913TT51435ZT80815C1B09CaucGT36866B9Empty_B9
UT57301WT51343WT51378ZT81387OT05888OT05899PT84225PT84236GT37828JT52076TT51483ZT80826C1B10CaucJT51211B10Empty_B10
UT57302WT51345WT51381MT94859OT05890OT05901PT84226PT84239ZT80932OT07280TT51511ZT80863C1B11CaucMT94829B11Empty_B11
UT57303WT51354WT51386MT94866OT05892PT84214PT84227PT84240GT37862PT85612TT51530ZT80865C1B12CaucMT94843B12Empty_B12
UT57310WT51355BC11352MT94868OT05893PT84215PT84228PT84241GT37864PT85658ZT80731ZT80869C1C01CaucGT38087C1Empty_C1
UT57312WT51358MT97172MT94869OT05894PT84216PT84230PT84242GT37869TT51399ZT80737ZT80870C1C02CaucGT38098C2Empty_C2
UT57317WT51359WA29584MT94875OT05896PT84222PT84231PT84243GT37888TT51407ZT80782ZT80925C1C03CaucJT52346C3Empty_C3
C1C04CaucMT97136C4Empty_C4
CMB2MT94892TT50701UT57287PT84244ZT79619PT84212ZT79617Y6Y15Y23Y3144C1C05CaucMT97158C5Empty_C5
MT94877MT94893TT50705UT57288PT84245PT84201PT84213ZT79618Y7Y16Y24Y32C1C06CaucTT51680C6Empty_C6
MT94880PT83505TT50708UT57292PT84247PT84202PT84248GT37853Y8Y17Y25Y33C1C07CaucZT81382C7Empty_C7
MT94882PT83535TT50720UT57293PT84256PT84206PT84249Y1Y9Y18Y26Y34C1C08CaucGT38075C8Empty_C8
MT94883PT83538TT50721UT57299TT50913PT84208PT84251Y2Y10Y19Y27Y35C1C09CaucGT36875C9Empty_C9
MT94884TT50697UT57281UT57635TT50916PT84209PT84252Y3Y12Y20Y28Y36C1C10CaucMT94803C10Empty_C10
MT94886TT50698UT57283OT06795TT50922PT84210PT84253Y4Y13Y21Y29Y37C1C11CaucMT94831C11Empty_C11
MT94888TT50700UT57286PC16856TT50923PT84211PT84254Y5Y14Y22Y30Y38265Should be 263C1C12CaucMT94846C12Empty_C12
C1D01CaucGT38089D1Empty_D1
C1D02CaucGT38100D2Empty_D2
C1D03CaucMT97121D3Empty_D3
C1D04CaucMT97139D4Empty_D4
C1D05CaucMT97159D5Empty_D5
C1D06CaucTT51682D6Empty_D6
C1D07CaucGT38065D7Empty_D7
C1D08CaucGT38076D8Empty_D8
C1D09CaucGT36877D9Empty_D9
C1D10CaucMT94807D10Empty_D10
C1D11CaucMT94833D11Empty_D11
C1D12CaucMT94848D12Empty_D12
C1E01CaucGT38091E1Empty_E1
C1E02CaucGT38106E2Empty_E2
C1E03CaucMT97122E3Empty_E3
C1E04CaucMT97141E4Empty_E4
C1E05CaucPT86478E5Empty_E5
C1E06CaucTT51683E6Empty_E6
C1E07CaucGT38066E7Empty_E7
C1E08CaucGT38078E8Empty_E8
C1E09CaucGT36878E9Empty_E9
C1E10CaucMT94815E10Empty_E10
C1E11CaucMT94834E11Empty_E11
C1E12CaucMT94850E12Empty_E12
C1F01CaucGT38092F1Empty_F1
C1F02CaucGT38107F2Empty_F2
C1F03CaucMT97123F3Empty_F3
C1F04CaucMT97145F4Empty_F4
C1F05CaucTT51669F5Empty_F5
C1F06CaucTT51684F6Empty_F6
C1F07CaucGT38067F7Empty_F7
C1F08CaucGT38081F8Empty_F8
C1F09CaucGT36884F9Empty_F9
C1F10CaucMT94817F10Empty_F10
C1F11CaucMT94835F11Empty_F11
C1F12CaucMT94853F12Empty_F12
C1G01CaucGT38093G1Empty_G1
C1G02CaucGT38108G2Empty_G2
C1G03CaucMT97124G3Empty_G3
C1G04CaucMT97150G4Empty_G4
C1G05CaucTT51675G5Empty_G5
C1G06CaucTT51685G6Empty_G6
C1G07CaucGT38069G7Empty_G7
C1G08CaucGT38083G8Empty_G8
C1G09CaucGT36885G9Empty_G9
C1G10CaucMT94818G10Empty_G10
C1G11CaucMT94838G11Empty_G11
C1G12CaucMT94855G12Empty_G12
C1H01CaucGT38094H1Empty_H1
C1H02CaucJA44327H2Empty_H2
C1H03CaucMT97125H3Empty_H3
C1H04CaucMT97152H4Empty_H4
C1H05CaucTT51676H5Empty_H5
C1H06CaucUT58303H6Empty_H6
C1H07CaucGT38070H7Empty_H7
C1H08CaucGC03394H8Empty_H8
C1H09CaucGT36886H9Empty_H9
C1H10CaucMT94826H10Empty_H10
C1H11CaucMT94839H11Empty_H11
C1H12CaucMT94858H12Empty_H12
C2A02CaucMT97185
C2A03CaucMT97199
C2A04CaucTT51702
C2A05CaucWT52470
C2A06CaucWT52486
C2A07CaucZT81380
C2A08CaucMT97167
C2A09CaucUA16894
C2A10CaucUA16921
C2A11CaucUT58298
C2A12CaucUT58318
C2B01CaucMT97173
C2B02CaucMT97186
C2B03CaucMT97200
C2B04CaucTT51703
C2B05CaucWT52471
C2B06CaucWT52490
C2B07CaucZT81381
C2B08CaucOT07753
C2B09CaucUA16895
C2B10CaucUA16924
C2B11CaucUT58299
C2B12CaucUT58319
C2C01CaucMT97176
C2C02CaucMT97187
C2C03CaucOT07803
C2C04CaucUT58333
C2C05CaucWT52472
C2C06CaucWT52493
C2C07CaucGT38114
C2C08CaucOT07760
C2C09CaucUA16896
C2C10CaucUA16927
C2C11CaucUT58300
C2C12CaucUT58320
C2D01CaucMT97177
C2D02CaucMT97188
C2D03CaucTT51689
C2D04CaucUT58334
C2D05CaucWT52474
C2D06CaucZC08844
C2D07CaucGT38119
C2D08CaucOT07767
C2D09CaucUA16897
C2D10CaucUA16928
C2D11CaucUT58301
C2D12CaucUT58321
C2E01CaucMT97178
C2E02CaucMT97189
C2E03CaucTT51693
C2E04CaucUT58335
C2E05CaucWT52477
C2E06CaucZT81337
C2E07CaucMT97163
C2E08CaucOT07776
C2E09CaucUA16899
C2E10CaucUA16929
C2E11CaucUT58302
C2E12CaucUT58324
C2F01CaucMT97179
C2F02CaucMT97192
C2F03CaucTT51694
C2F04CaucUT58336
C2F05CaucWT52480
C2F06CaucZT81342
C2F07CaucMT97164
C2F08CaucOT07785
C2F09CaucUA16903
C2F10CaucUC10177
C2F11CaucUT58314
C2F12CaucWA29566
C2G01CaucMT97180
C2G02CaucMT97195
C2G03CaucTT51696
C2G04CaucUT58337
C2G05CaucWT52482
C2G06CaucZT81372
C2G07CaucMT97165
C2G08CaucPT86536
C2G09CaucUA16908
C2G10CaucUC10178
C2G11CaucUT58315
C2G12CaucWA29572
C2H01CaucMT97184
C2H02CaucMT97196
C2H03CaucTT51698
C2H04CaucWT52457
C2H05CaucWT52485
C2H06CaucZT81377
C2H07CaucMT97166
C2H08CaucUA16891
C2H09CaucUA16918
C2H10CaucUT58295
C2H11CaucUT58317
C2H12CaucWA29583
Combo1A02CaucUT57318
Combo1A03CaucWT51362
Combo1A04CaucWA29594
Combo1A05AAJT51471
Combo1A06AAOT05897
Combo1A07AAPT84223
Combo1A08AAPT84232
Combo1A09HispGT37778
Combo1A10HispGT37900
Combo1A11HispTT51422
Combo1A12HispZT80786
Combo1B01CaucUT57300
Combo1B02CaucWT51342
Combo1B03CaucWT51373
Combo1B04CaucWA29612
Combo1B05AAJT51499
Combo1B06AAOT05898
Combo1B07AAPT84224
Combo1B08AAPT84234
Combo1B09HispGT37812
Combo1B10HispGT37913
Combo1B11HispTT51435
Combo1B12HispZT80815
Combo1C01CaucUT57301
Combo1C02CaucWT51343
Combo1C03CaucWT51378
Combo1C04CaucZT81387
Combo1C05AAOT05888
Combo1C06AAOT05899
Combo1C07AAPT84225
Combo1C08AAPT84236
Combo1C09HispGT37828
Combo1C10HispJT52076
Combo1C11HispTT51483
Combo1C12HispZT80826
Combo1D01CaucUT57302
Combo1D02CaucWT51345
Combo1D03CaucWT51381
Combo1D04CaucMT94859
Combo1D05AAOT05890
Combo1D06AAOT05901
Combo1D07AAPT84226
Combo1D08AAPT84239
Combo1D09HispZT80932
Combo1D10HispOT07280
Combo1D11HispTT51511
Combo1D12HispZT80863
Combo1E01CaucUT57303
Combo1E02CaucWT51354
Combo1E03CaucWT51386
Combo1E04CaucMT94866
Combo1E05AAOT05892
Combo1E06AAPT84214
Combo1E07AAPT84227
Combo1E08AAPT84240
Combo1E09HispGT37862
Combo1E10HispPT85612
Combo1E11HispTT51530
Combo1E12HispZT80865
Combo1F01CaucUT57310
Combo1F02CaucWT51355
Combo1F03CaucBC11352
Combo1F04CaucMT94868
Combo1F05AAOT05893
Combo1F06AAPT84215
Combo1F07AAPT84228
Combo1F08AAPT84241
Combo1F09HispGT37864
Combo1F10HispPT85658
Combo1F11HispZT80731
Combo1F12HispZT80869
Combo1G01CaucUT57312
Combo1G02CaucWT51358
Combo1G03CaucMT97172
Combo1G04CaucMT94869
Combo1G05AAOT05894
Combo1G06AAPT84216
Combo1G07AAPT84230
Combo1G08AAPT84242
Combo1G09HispGT37869
Combo1G10HispTT51399
Combo1G11HispZT80737
Combo1G12HispZT80870
Combo1H01CaucUT57317
Combo1H02CaucWT51359
Combo1H03CaucWA29584
Combo1H04CaucMT94875
Combo1H05AAOT05896
Combo1H06AAPT84222
Combo1H07AAPT84231
Combo1H08AAPT84243
Combo1H09HispGT37888
Combo1H10HispTT51407
Combo1H11HispZT80782
Combo1H12HispZT80925
Combo2A02CaucMT94892
Combo2A03CaucTT50701
Combo2A04CaucUT57287
Combo2A05AAPT84244
Combo2A06AAZT79619
Combo2A07AAPT84212
Combo2A08AAZT79617
Combo2A09CaucY6
Combo2A10AAY15
Combo2A11HispY23
Combo2A12CaucY31
Combo2B01CaucMT94877
Combo2B02CaucMT94893
Combo2B03CaucTT50705
Combo2B04CaucUT57288
Combo2B05AAPT84245
Combo2B06AAPT84201
Combo2B07AAPT84213
Combo2B08AAZT79618
Combo2B09CaucY7
Combo2B10AAY16
Combo2B11HispY24
Combo2B12CaucY32
Combo2C01CaucMT94880
Combo2C02CaucPT83505
Combo2C03CaucTT50708
Combo2C04CaucUT57292
Combo2C05AAPT84247
Combo2C06AAPT84202
Combo2C07AAPT84248
Combo2C08HispGT37853
Combo2C09CaucY8
Combo2C10AAY17
Combo2C11HispY25
Combo2C12AAY33
Combo2D01CaucMT94882
Combo2D02CaucPT83535
Combo2D03CaucTT50720
Combo2D04CaucUT57293
Combo2D05AAPT84256
Combo2D06AAPT84206
Combo2D07AAPT84249
Combo2D08CaucY1
Combo2D09CaucY9
Combo2D10AAY18
Combo2D11HispY26
Combo2D12AAY34
Combo2E01CaucMT94883
Combo2E02CaucPT83538
Combo2E03CaucTT50721
Combo2E04CaucUT57299
Combo2E05AATT50913
Combo2E06AAPT84208
Combo2E07AAPT84251
Combo2E08CaucY2
Combo2E09CaucY10
Combo2E10AAY19
Combo2E11HispY27
Combo2E12AAY35
Combo2F01CaucMT94884
Combo2F02CaucTT50697
Combo2F03CaucUT57281
Combo2F04AsianUT57635
Combo2F05AATT50916
Combo2F06AAPT84209
Combo2F07AAPT84252
Combo2F08CaucY3
Combo2F09CaucY12
Combo2F10HispY20
Combo2F11HispY28
Combo2F12AAY36
Combo2G01CaucMT94886
Combo2G02CaucTT50698
Combo2G03CaucUT57283
Combo2G04AsianOT06795
Combo2G05AATT50922
Combo2G06AAPT84210
Combo2G07AAPT84253
Combo2G08CaucY4
Combo2G09AAY13
Combo2G10HispY21
Combo2G11HispY29
Combo2G12AAY37
Combo2H01CaucMT94888
Combo2H02CaucTT50700
Combo2H03CaucUT57286
Combo2H04AsianPC16856
Combo2H05AATT50923
Combo2H06AAPT84211
Combo2H07AAPT84254
Combo2H08CaucY5
Combo2H09AAY14
Combo2H10HispY22
Combo2H11HispY30
Combo2H12HispY38
Analysis-AFDIL
Variant listName of ProfileSampleHaplogroupMissing MutationsPrivate MutationsContinentRegion
C1B01CaucGT38086263G 315.1C 477C 750G 1438G 3010A 4767G 4769G 8860G 15326G 16189C 16519CH1c21GT38086H1c21noneT16189CEurope (H)
C1C01CaucGT3808773G 146C 263G 309.1C 309.2C 315.1C 458T 709A 750G 930A 1438G 1709A 1888A 2706G 4216C 4769G 4917G 5147A 7028T 8697A 8730G...T2b6bGT38087T2b6bnonenoneEuropeSpain
C1D01CaucGT3808973G 185A 228A 263G 295T 309.1C 315.1C 462T 489C 750G 1438G 2706G 3010A 4216C 4769G 7028T 8860G 10084C 11251G 11719A 1261...J1c8aGT38089J1c8anoneT16189CEuropePoland, Germany, Serbia, Uzbekistan
C1E01CaucGT3809172C 263G 309.1C 315.1C 750G 1438G 2706G 4580A 4769G 7028T 8860G 10933T 15326G 15467G 15904T 16298CEuropeGT38091VnoneC10933T A15467GEuropeSpain, Slovakia, Hungary
C1F01CaucGT38092198T 263G 315.1C 456T 524.1A 524.2C 524.3A 524.4C 722T 750G 1438G 4769G 8343G 8860G 9327G 12771A 13434G 13801G 15326G 15...H5e1a1GT38092H5e1a1noneC198T A9327G A13801G T15670CEurope (H)
C1G01CaucGT38093150T 263G 315.1C 750G 1438G 3010A 4769G 8349T 8860G 14053G 15326G 16355T 16519C>JQ702360.1GT38093H1ononenoneEuropePortugal
C1H01CaucGT38094263G 309.1C 315.1C 750G 1438G 4502C 4769G 8860G 9948A 11252G 15326G 15784C 16519C>HM625709.1GT38094H65noneA11252GEurope (H)
C1A02CaucGT3809573G 199C 203A 204C 250C 263G 309.1C 315.1C 455.1T 709A 750G 1438G 1719A 2706G 3447G 3990T 4529T 4769G 6734A 7028T 8251A ...I1a1bGT38095I1a1b-573.1C G709A C9727TEurope (I1a1)
C1B02CaucGT3809773G 114T 263G 315.1C 497T 750G 1189C 1438G 1811G 2706G 3480G 4769G 7028T 8027A 8860G 9055A 9698C 10398G 10550G 11299C 11...K1a1b1GT38097K1a1b1noneG8027A G15301AEuropeSlovakia, Hungary
C1C02CaucGT38098152C 263G 315.1C 523del 524del 750G 1438G 3010A 3796G 4769G 8860G 15326G 15519A 16111T 16189C 16356C 16519C>JQ704003.1GT38098H1b1A16183C -309.1C -309.2C C16111T T152CEuropeGermany, Romania
C1D02CaucGT38100263G 309.1C 315.1C 750G 1438G 3010A 4655A 4769G 8860G 12354C 15326G 16189C 16519C>JQ704300.1GT38100H1none-309.1C G4655AEuropeSpain, Germany, Poland, Romania
C1E02CaucGT38106263G 309.1C 315.1C 2416C 8817GH2a2aGT38106H2a2anoneT2416C A8817GEuropeSpain
C1F02CaucGT3810773G 263G 309.1C 315.1C 750G 1438G 1700C 2706G 3197C 3388A 4769G 5495C 7028T 8788T 8860G 9477A 11467G 11719A 12308G 12372...U5a1a1GT38107U5a1a1noneC3388A C8788TEuropeSpain, Romania, Serbia
C1G02CaucGT38108263G 309.1C 309.2C 315.1C 750G 1438G 3010A 4373C 4769G 8860G 15313C 15326G 16189C 16519CH1+16189GT38108H1+16189noneT4373C T15313CEuropeAll areas
C1H02CaucJA4432773G 152C 199C 204C 207A 250C 263G 315.1C 750G 1438G 1719A 2706G 4529T 4769G 7028T 8251A 8860G 10034C 10238C 10398G 11719...I2JA44327I2-573.1C G16474TEurope (I)
C1A03CaucJM2831573G 146C 152C 263G 315.1C 709A 750G 1438G 1811G 2706G 3480G 4561C 4769G 7028T 8860G 9055A 9698C 9716C 10550G 11299C 1146...>JQ705301.1JM28315K2a6-309.1C noneEuropeSpain
C1B03CaucJT5234573G 263G 309.1C 315.1C 456T 523del 524del 750G 1438G 2851G 4095T 4336C 4769G 8860G 9055A 13194A 15326G 15833T 16138G 163...H5a1c1aJT52345H5a1c1anoneA16138G A73GEuropeCentral and Eastern
C1C03CaucJT52346146C 263G 309.1C 309.2C 315.1C 456T 750G 1438G 4769G 8860G 15326G 16292T 16304C 16325C>JQ702019.1JT52346H5gnonenoneEuropeSpain
C1D03CaucMT9712173G 185A 188G 228A 263G 295T 309.1C 315.1C 462T 489C 750G 1438G 2706G 3010A 4216C 4769G 7028T 7762A 8860G 10398G 11251G ...J1c2MT97121J1c2noneT16093C G7762AEuropeRomania
C1E03CaucMT9712273G 152C 263G 315.1C 709A 750G 930A 1438G 1888A 2706G 4216C 4769G 4917G 5147A 7028T 8697A 8860G 10463C 11242G 11251G 117...>EU683970.1MT97122T2b2bnonenoneEuropeBulgaria, Serbia
C1F03CaucMT9712373G 152C 195C 263G 315.1C 709A 750G 1438G 1888A 2706G 4216C 4769G 4917G 7028T 8697A 8860G 9899C 10463C 11251G 11719A 126...T1a1MT97123T1a1noneA16158GEurope (T1a)
C1G03CaucMT9712473G 263G 309.1C 315.1C 497T 524.1A 524.2C 524.3A 524.4C 750G 1189C 1438G 1811G 2706G 3480G 4769G 4961G 7028T 7337A 8860G...>JQ705445.1MT97124K1aT16093C -309.1C -524.3A -524.4CEuropeSlovakia
C1H03CaucMT9712573G 152C 263G 309.1C 315.1C 523del 524del 750G 1438G 2706G 3197C 3750T 4769G 7028T 7843G 7978T 8104C 8860G 9148C 9477A 1...U5a2d1aMT97125U5a2d1anoneT152CEurope (U5a)All areas
C1A04CaucMT9712673G 150T 263G 309.1C 315.1C 750G 1438G 1811G 2294G 2706G 3010A 4703C 4769G 6518T 7028T 8860G 9266A 10506G 11467G 11719A ...U3a1cMT97126U3a1cnoneT16342C
C1B04CaucMT9713173G 228A 263G 295T 315.1C 462T 482C 489C 750G 1438G 2706G 3010A 3394C 4216C 4769G 7028T 8860G 9635C 10398G 11116C 11251G...J1c1aMT97131J1c1anoneT11116C C12346T
C1C04CaucMT9713616T 73G 150T 199C 263G 309.1C 315.1C 497T 750G 1189C 1438G 1811G 2706G 3480G 4769G 7028T 7519del 8281del 8282del 8283del...K1a11bMT97136K1a11bnoneA16215G A7519-
C1D04CaucMT9713973G 150T 152C 195C 215G 263G 295T 310.1T 315.1C 319C 489C 513A 750G 1438G 1850C 2706G 3447G 4216C 4769G 6731C 7028T 7476...J2a1a1a2MT97139J2a1a1a2noneT6731C
C1E04CaucMT9714173G 146C 153G 195C 225A 226C 263G 315.1C 524.1A 524.2C 750G 1438G 1719A 2706G 4769G 6221C 6371T 7028T 8393T 8425G 8860G ...>JQ702482.1MT97141X2b+226-309.1C -524.1A -524.2C
C1F04CaucMT9714573G 152C 195C 263G 315.1C 499A 524.1A 524.2C 750G 961C 1438G 1811G 2706G 4646C 4769G 5999C 6047G 7028T 8818T 8860G 11332...U4a1aMT97145U4a1anonenone
C1G04CaucMT97150146C 263G 309.1C 309.2C 315.1C 456T 750G 1438G 4336C 4769G 8860G 9053A 15326G 15833T 16304C 16311C>JQ705315.1MT97150H5a1noneT146C -309.2C
C1H04CaucMT97152263G 309.1C 315.1C 750G 1438G 4769G 6776C 8084T 8860G 15326G 16519C>JQ702808.1MT97152H3nonenone
C1A05CaucMT9715573G 263G 309.1C 315.1C 524.1A 524.2C 709A 750G 960.1C 1438G 1888A 2706G 2850C 4216C 4769G 4917G 6632C 7022C 7028T 8697A ...>AY495304.1MT97155T2a1anone-524.1A -524.2C -960.1C
C1B05CaucMT9715673G 152C 195C 198T 263G 309.1C 315.1C 709A 750G 1438G 1888A 2706G 4216C 4769G 4917G 7028T 7870C 8697A 8860G 9899C 10463C...T1a1MT97156T1a1noneC198T T7870C
C1C05CaucMT9715873G 152C 195C 263G 309.1C 315.1C 709A 750G 1438G 1888A 2706G 4216C 4769G 4917G 7028T 8697A 8860G 9899C 10463C 11251G 117...T1a1MT97158T1a1nonenone
C1D05CaucMT97159263G 309.1C 315.1C 750G 1438G 2259T 4745G 4769G 8860G 13680T 14560A 14872T 15326G 16129A>AY495149.1MT97159H13a1anonenone
C1E05CaucPT86478263G 309.1C 315.1C 750G 1438G 3010A 4769G 5460A 7711C 8860G 12070A 15326G 15817G 16519CH1e2aPT86478H1e2anoneT7711C
C1F05CaucTT51669263G 309.1C 309.2C 315.1C 477C 750G 1438G 3010A 4769G 5318T 8860G 12858T 15326G 16519CH1c2TT51669H1c2noneC5318T
C1G05CaucTT5167573G 263G 315.1C 750G 1438G 2706G 3197C 4769G 7028T 8860G 9477A 9667G 11467G 11719A 12308G 12372A 13617C 14766T 14793G 15...U5a1b1TT51675U5a1b1nonenone
C1H05CaucTT51676263G 309.1C 315.1C 456T 750G 1438G 3666A 4769G 5302C 8860G 15326G 16304C 16311C 16391A>JQ703266.1TT51676H5snonenone
C1A06CaucTT51677263G 309.1C 309.2C 315.1C 750G 1438G 4769G 8860G 13830C 14470A 15326G 16093C 16124C 16221T 16519C>JQ703002.1TT51677H10e1nonenone
C1B06CaucTT5167973G 263G 315.1C 709A 750G 1438G 1888A 2706G 2850C 4216C 4769G 4917G 7022C 7028T 8697A 8860G 10463C 11251G 11719A 11812G ...T2a1aTT51679T2a1anonenone
C1C06CaucTT5168072C 73G 152C 263G 315.1C 537T 750G 1438G 2706G 4580A 4769G 7028T 8860G 13105G 14770T 15326G 15904T 16086C 16298CV2bTT51680V2bnoneT16086C A73G T152C C537T
C1D06CaucTT5168273G 150T 152C 195C 215G 263G 295T 310.1T 315.1C 319C 489C 513A 750G 1438G 1850C 2706G 3447G 4216C 4769G 7028T 7476T 7789...J2a1a1a2TT51682J2a1a1a2C16261T none
C1E06CaucTT5168373G 151T 263G 309.1C 315.1C 709A 750G 930A 1438G 1888A 2706G 4216C 4769G 4917G 5147A 7028T 8697A 8860G 9809G 10463C 1075...>JQ702951.1TT51683T2b3enonenone
C1F06CaucTT51684263G 309.1C 315.1C 523del 524del 750G 1438G 3010A 4769G 8860G 15314A 15326G 15924G 16519C>HM000002.1TT51684H1+16311T16311C none
C1G06CaucTT5168573G 143A 153G 195C 200G 263G 309.1C 315.1C 750G 1438G 1719A 2706G 3552C 4769G 6221C 6371T 6680C 7028T 7299G 8422G 8860G ...X2a1b1aTT51685X2a1b1anonenone
C1H06CaucUT58303143A 263G 315.1C 750G 1438G 3010A 3666A 4769G 5393C 5899.1C 8860G 15326G 16239A 16519CH1ak1UT58303H1ak1noneC16239A G143A -5899.1C
Group 49to96
C1H08CaucGC03394152C 263G 309.1C 315.1C 750G 1438G 1809C 4769G 8718G 8860G 9299G 15326G 16519CH86H86noneT152C A8718G A9299GEurope (H)
C1A09CaucGT36864Not analyzed on first pass
C1B09CaucGT3686673G 210G 263G 309.1C 315.1C 750G 1438G 3010A 4769G 6365C 8860G 15326G 16162G 16209C 16278T 16519CH1a1H1a1noneC16278T A210GEuropeRomania
C1C09CaucGT3687573G 152C 195C 263G 309.1C 315.1C 499A 750G 73G 152C 263G 315.1C 709A 750G 1438G 1888A 2706G 4216C 4769G 4904T 4917G 5964...T1a5T1a5A16163G T16093C A16399G T152C C4904T T5964C A10502G T11569CEuropeRomania
C1D09CaucGT36877263G 315.1C 456T 523del 524del 750G 1438G 4336C 4769G 8860G 11719A 15326G 15833T 16304CH5a1bH5a1bnonenoneEurope (H)Germany, Poland
C1E09CaucGT36878152C 263G 315.1C 750G 1438G 4769G 8860G 10394T 14155T 14869C 15326G 16519CH16dH16dnonenoneEurope (H)
C1F09CaucGT3688473G 150T 152C 195C 215G 263G 295T 310.1T 315.1C 319C 489C 513A 750G 1438G 1850C 2706G 3447G 4216C 4769G 7028T 7476T 7789..J2a1a1a2J2a1a1a2nonenone
C1G09CaucGT3688573G 152C 195C 263G 309.1C 315.1C 499A 750G 73G 152C 185A 263G 295T 315.1C 462T 489C 750G 1438G 2706G 3010A 4216C 4769G 7...J1c3bJ1c3bnoneT152C T195C G499A
C1H09CaucGT3688673G 152C 195C 263G 309.1C 315.1C 499A 750G 1438G 1811G 2706G 4646C 4769G 5999C 6047G 7028T 8155A 8818T 8860G 11332T 1146...U4a1cU4a1cnonenone
C1D07CaucGT3806573G 152C 195C 263G 309.1C 315.1C 499A 750G 73G 152C 263G 315.1C 709A 750G 1438G 1888A 73G 195C 263G 315.1C 523del 524del...>JQ705993.1H1a3bnoneA16241C T152C -309.1C G499A G709A G1888A
C1E07CaucGT3806673G 152C 195C 263G 309.1C 315.1C 499A 750G 73G 152C 195C 263G 309.1C 315.1C 709A 750G 1438G 1888A 2706G 4216C 4769G 4917...T1a1T1a1noneG499A
C1F07CaucGT3806773G 143A 189G 192C 194T 195C 207A 263G 309.1C 315.1C 489C 709A 750G 1243C 1438G 2706G 3505G 4769G 5046A 5460A 7028T 8251...W9W9T204C G143A T192C T489C
C1G07CaucGT38069263G 315.1C 524.1A 524.2C 750G 1438G 4769G 4793G 8860G 15326G 16355T 16519C>JQ705594.1H7none-524.1A -524.2C
C1H07CaucGT38070263G 309.1C 315.1C 750G 1438G 2706G 4769G 7028T 8860G 9801A 10205T 10920T 15326G 15514C 16311C>HQ384193.1HV+16311nonenone
C1A08CaucGT38072Not analyzed on first pass
C1B08CaucGT3807373G 146C 195C 263G 310C 315del 499A 524.1A 524.2C 750G 1438G 1811G 2706G 4646C 4769G 5999C 6047G 7028T 8818T 8860G 10172...U4a2U4a2noneT146C C315- G10172A
C1C08CaucGT38075263G 315.1C 750G 1438G 4769G 4793G 8860G 15326G 16355T 16519C>JQ705594.1H7nonenone
C1D08CaucGT3807673G 185A 189G 203A 204C 263G 309.1C 315.1C 750G 1438G 1700C 2706G 3197C 4769G 5495C 7028T 8860G 9477A 11467G 11719A 1230...>JQ705318.1U5a1a1dnoneG203A
C1E08CaucGT38078263G 315.1C 750G 1438G 4769G 8860G 10394T 11887A 15043A 15326G 16519CH16H16noneG11887A G15043A
C1F08CaucGT38081263G 309.1C 315.1C 750G 1438G 2706G 4580A 4769G 7028T 8860G 10609C 12810G 15181G 15326G 15904T 16216G 16298CV3cV3cT72C T10609C A15181G
C1G08CaucGT38083196C 263G 309.1C 315.1C 750G 1438G 4769G 8860G 9545G 11152C 12651A 13500C 14203G 15326G 16519CH26a1a1H26a1a1nonenone
C1A10CaucJT51178263G 293C 315.1C 750G 1438G 4769G 6776C 8860G 8937C 12346T 15326G 15530C 16209C 16519C>JQ703690.1H3z1nonenone
C1B10CaucJT5121173G 263G 315.1C 750G 1438G 2706G 3348G 3969T 4172A 4769G 7028T 7805A 8754T 8860G 11467G 11719A 11938T 12308G 12372A 1370...>JQ702612.1U6a1a1-309.1C none
C1C10CaucMT9480373G 263G 309.1C 315.1C 750G 1438G 3010A 4769G 6365C 8860G 15326G 16162G 16209C 16519CH1a1H1a1nonenone
C1D10CaucMT9480773G 152C 195C 263G 309.1C 315.1C 709A 750G 1438G 1888A 2706G 4216C 4769G 4917G 7028T 8697A 8860G 9120G 9899C 10463C 1125...>JQ703894.1T1a1cnonenone
C1E10CaucMT94815152C 263G 309.1C 315.1C 709A 750G 1438G 3010A 4769G 8200C 8860G 9101C 15326G 16519CH30b1H30b1nonenone
C1F10CaucMT9481773G 152C 199C 204C 263G 315.1C 669C 750G 1438G 1719A 2702A 2706G 3336C 4769G 5315G 7028T 8860G 8901G 10238C 10398G 10598...>JQ704871.1N1a1a1a3-573.1C -573.2C -573.3C none
C1G10CaucMT94818263G 309.1C 315.1C 750G 1193C 1438G 2706G 4204C 4769G 5581G 7028T 8860G 12492T 12599C 15326G 16311C 16519C>JQ702536.1HV16nonenone
C1H10CaucMT9482673G 242T 263G 295T 309.1C 315.1C 462T 489C 750G 1438G 2158C 2706G 3010A 4216C 4769G 5460A 5463T 6911C 7028T 8269A 8557A ...>HQ286325.1J1b1a1aG16390A none
C1A11CaucMT94827146C 195C 263G 315.1C 750G 961G 1438G 4769G 7278C 8227C 8448C 8860G 13759A 15326G 16293G 16311C>JQ703593.1H11anonenone
C1B11CaucMT94829146C 195C 249del 263G 309.1C 315.1C 750G 961G 1438G 4769G 8448C 8860G 8898T 13759A 15326G 16278T 16293G 16311C>GU122994.1H11a1noneA249- -309.1C
C1C11CaucMT9483173G 263G 309.1C 315.1C 497T 524.1A 524.2C 750G 1189C 1438G 1811G 2706G 3480G 4769G 5773A 7028T 8860G 9055A 9698C 10398G ...K1a2aK1a2anoneG16145A T10786C
C1D11CaucMT9483373G 152C 263G 315.1C 533G 709A 750G 1438G 1842G 1888A 2695A 2706G 4216C 4769G 4917G 6261A 7028T 8455T 8697A 8860G 10463C...T2c1aT2c1a-573.1C T16172C C16266T T152C A533G A1842G G2695A C13770T G13928C
C1E11CaucMT9483473G 263G 315.1C 709A 750G 930A 1438G 1888A 2706G 4216C 4769G 4917G 5147A 7028T 8697A 8860G 10463C 11251G 11719A 11812G 1...T2bT2bnoneT13488C
C1F11CaucMT9483573G 146C 242T 263G 295T 309.1C 315.1C 462T 489C 750G 1438G 2158C 2706G 3010A 4216C 4769G 5460A 7028T 8269A 8557A 8860G 1...>JQ704626.1J1b1a1nonenone
C1G11CaucMT94838263G 593C 750G 1438G 4769G 6296T 14869A 15326G 16129A 16519C>AY495154.1H17a2-309.1C -315.1C G3915A A8860G none
C1H11CaucMT9483973G 228A 234G 263G 315.1C 709A 750G 930A 1438G 1888A 2706G 4216C 4769G 4917G 5147A 7028T 8697A 8860G 10463C 11251G 11719...>HM055613.1T2b-309.1C A234G G11914A
C1A12CaucMT94842263G 309.1C 315.1C 750G 1438G 3010A 4769G 8860G 15326G 16189C 16356C 16519CH1bH1bnonenone
C1B12CaucMT9484373G 152C 217C 263G 309.1C 315.1C 340T 508G 523del 524del 750G 1438G 1811G 2526T 2706G 3720G 4769G 5390G 5426C 6045T 6152...>EF452294.1U2e1enonenone
C1C12CaucMT9484654.1C 56C 93G 263G 309.1C 315.1C 573.1C 573.2C 750G 1438G 4769G 6253C 8860G 11410C 14953T 15326GH15a1H15a1T55C T57C -54.1C A56C A93G -573.1C -573.2C
C1D12CaucMT94848152C 195C 257G 263G 309.1C 309.2C 315.1C 477C 750G 1438G 3010A 3172T 4769G 8473C 8860G 15326G 16519C>HM625701.1H1c3none-309.2C C3172T
C1E12CaucMT94850263G 309.1C 309.2C 315.1C 750G 1438G 3010A 4769G 8860G 15326G 16189C 16298C 16519C>HQ659690.1H1+16189nonenone
C1F12CaucMT9485373G 263G 309.1C 315.1C 321C 709A 750G 1438G 1888A 2706G 4216C 4769G 4917G 5147A 5426C 6137C 7028T 8572A 8697A 8860G 1046...T2b24aT2b24aG930A T16445C T6137C
C1G12CaucMT9485573G 143A 189G 192C 194T 195C 196C 204C 207A 263G 315.1C 709A 750G 1243C 1438G 2706G 3505G 3531A 4769G 5046A 5460A 7028T ...W4a1W4a1nonenone
C1H12CaucMT9485873G 152C 263G 309.1C 315.1C 523del 524del 750G 921C 1438G 2706G 3203G 4659A 4769G 5147A 5372G 6680C 7028T 7424G 8618C 87...L3d1c1L3d1c1noneG4659A
C1A07CaucUT5830573G 151T 152C 263G 309.1C 315.1C 709A 750G 930A 1438G 1888A 2706G 4216C 4769G 4917G 5147A 7028T 8697A 8860G 10463C 10750...T2b3+151T2b3+151noneT16311C G16390A T152C T11253C
C1B07CaucUT5831073G 185A 188G 228A 263G 295T 309.1C 315.1C 462T 489C 523del 524del 750G 1438G 2706G 3010A 4216C 4769G 6620C 7028T 8860G ...J1c2dJ1c2dnonenone
C1C07CaucZT8138273G 185A 188G 228A 263G 295T 309.1C 315.1C 263G 315.1C 456T 750G 1438G 2626C 4769G 7424G 8020A 8860G 11161T 15326G 16304...H5kH5knoneA73G G185A A188G G228A C295T A7424G C11161T
https://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypes
Sheet2
SampleMissing MutationsPrivate MutationsHaplogroupContinent
GT38086noneT16189CH1c21Europe (H)
GT38087nonenoneT2b6bEurope
GT38089noneT16189CJ1c8aEurope
GT38091noneC10933T A15467GVEurope
GT38092noneC198T A9327G A13801G T15670CH5e1a1Europe (H)
GT38093nonenoneH1oEurope
GT38094noneA11252GH65Europe (H)
GT38095-573.1C G709A C9727TI1a1bEurope (I1a1)
GT38097noneG8027A G15301AK1a1b1Europe
GT38098A16183C -309.1C -309.2C C16111T T152CH1b1Europe
GT38100none-309.1C G4655AH1Europe
GT38106noneT2416C A8817GH2a2aEurope
GT38107noneC3388A C8788TU5a1a1Europe
GT38108noneT4373C T15313CH1+16189Europe
JA44327-573.1C G16474TI2Europe (I)
JM28315-309.1C noneK2a6Europe
JT52345noneA16138G A73GH5a1c1aEurope
JT52346nonenoneH5gEurope
MT97121noneT16093C G7762AJ1c2Europe
MT97122nonenoneT2b2bEurope
MT97123noneA16158GT1a1Europe (T1a)
MT97124T16093C -309.1C -524.3A -524.4CK1aEurope
MT97125noneT152CU5a2d1aEurope (U5a)
https://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypeshttps://empop.online/haplotypes
AnalysisQ25-ILMN
GM Excess HP CallsGM Missed VariantsCommentComment2
Group 1to48Matches in DBSourceName of ProfileHaplogroupMissing MutationsPrivate MutationsQuery
C1B01CaucGT38086PhylotreeH1c21H1c21noneT16189C263G 309.1C 315.1C 477C 750G 1438G 3010A 4767G 4769G 8860G 15326G 16189C 16519C
C1C01CaucGT38087PhylotreeT2b6bT2b6bnonenone73G 146C 263G 309.1C 309.2C 315.1C 458T 709A 750G 930A 1438G 1709A 1888A 2706G 4216C 4769G 4917G 5147A 7028T 8697A 8730G...
C1D01CaucGT38089PhylotreeJ1c8aJ1c8anoneT16189C73G 185A 228A 263G 295T 309.1C 315.1C 462T 489C 750G 1438G 2706G 3010A 4216C 4769G 7028T 8860G 10084C 11251G 11719A 1261...
C1E01CaucGT38091PhylotreeVVnoneC10933T A15467G72C 263G 309.1C 315.1C 750G 1438G 2706G 4580A 4769G 7028T 8860G 10933T 15326G 15467G 15904T 16298C
C1F01CaucGT38092PhylotreeH5e1a1H5e1a1noneC198T A9327G A13801G T15670C198T 263G 315.1C 456T 524.1A 524.2C 524.3A 524.4C 722T 750G 1438G 4769G 8343G 8860G 9327G 12771A 13434G 13801G 15326G 15...
C1G01CaucGT38093GenBank>JQ702360.1H1ononenone150T 263G 315.1C 750G 1438G 3010A 4769G 8349T 8860G 14053G 15326G 16355T 16519C
C1H01CaucGT38094PhylotreeH65H65noneG9948A A11252G263G 309.1C 315.1C 750G 1438G 4769G 8860G 9948A 11252G 15326G 15784C 16519C
C1A02CaucGT38095PhylotreeI1a1bI1a1b-573.1CG709A C9727T73G 199C 203A 204C 250C 263G 309.1C 315.1C 455.1T 709A 750G 1438G 1719A 2706G 3447G 3990T 4529T 4769G 6734A 7028T 8251A ...
C1B02CaucGT38097PhylotreeK1a1b1K1a1b1noneG8027A G15301A73G 114T 263G 315.1C 497T 750G 1189C 1438G 1811G 2706G 3480G 4769G 7028T 8027A 8860G 9055A 9698C 10398G 10550G 11299C 11...
C1C02CaucGT38098Missing regions - insufficient quality?GenBank>JQ704003.1H1b1A16183C -309.1C -309.2CC16111T T152C152C 263G 315.1C 523del 524del 750G 1438G 3010A 3796G 4769G 8860G 15326G 15519A 16111T 16189C 16356C 16519C
C1D02CaucGT38100GenBank>JQ704300.1H1none-309.1C G4655A263G 309.1C 315.1C 750G 1438G 3010A 4655A 4769G 8860G 12354C 15326G 16189C 16519C
C1E02CaucGT38106PhylotreeH2a2aH2a2anoneT2416C A8817G263G 309.1C 315.1C 2416C 8817G
C1F02CaucGT38107PhylotreeU5a1a1U5a1a1noneC3388A C8788T73G 263G 309.1C 315.1C 750G 1438G 1700C 2706G 3197C 3388A 4769G 5495C 7028T 8788T 8860G 9477A 11467G 11719A 12308G 12372...
C1G02CaucGT38108GenBank>JQ704557.1H1+16239C16239T T152C -309.1CT4373C A10840G263G 315.1C 750G 1438G 3010A 4373C 4769G 8860G 10840G 15313C 15326G 16519C
C1H02CaucJA44327Appears to be 1:1 mixture with some shared variantsrerunPhylotreeI2I2G16129A T199C -573.1C G1719A A2706G A4529T C7028T G8251Anone73G 152C 204C 207A 250C 263G 315.1C 750G 1438G 4769G 8860G 10034C 10238C 10398G 11719A 12501A 12705T 13780G 14766T 15043...
C1A03CaucJM28315GenBank>JQ705301.1K2a6-309.1Cnone73G 146C 152C 263G 315.1C 709A 750G 1438G 1811G 2706G 3480G 4561C 4769G 7028T 8860G 9055A 9698C 9716C 10550G 11299C 1146...
C1B03CaucJT52345PhylotreeH5a1c1aH5a1c1anoneA16138G A73G73G 263G 309.1C 315.1C 456T 523del 524del 750G 1438G 2851G 4095T 4336C 4769G 8860G 9055A 13194A 15326G 15833T 16138G 163...
C1C03CaucJT52346GenBank>JQ702019.1H5gnonenone146C 263G 309.1C 309.2C 315.1C 456T 750G 1438G 4769G 8860G 15326G 16292T 16304C 16325C
C1D03CaucMT97121Missing coverage in region 13669-13758 (Amp1 low)PhylotreeJ1c2J1c2G13708AT16093C G7762A73G 185A 188G 228A 263G 295T 309.1C 315.1C 462T 489C 750G 1438G 2706G 3010A 4216C 4769G 7028T 7762A 8860G 10398G 11251G ...
C1E03CaucMT97122GenBank>EU683970.1T2b2bnonenone73G 152C 263G 315.1C 709A 750G 930A 1438G 1888A 2706G 4216C 4769G 4917G 5147A 7028T 8697A 8860G 10463C 11242G 11251G 117...
C1F03CaucMT97123Possible 80/20 mixturererunPhylotreeT1a1T1a1noneA16158G73G 152C 195C 263G 315.1C 709A 750G 1438G 1888A 2706G 4216C 4769G 4917G 7028T 8697A 8860G 9899C 10463C 11251G 11719A 126...
C1G03CaucMT97124PhylotreeK1aK1aA2706G A3480G C7028T G9055AC16256T T15479C73G 263G 309.1C 315.1C 497T 524.1A 524.2C 524.3A 524.4C 750G 1189C 1438G 1811G 4769G 8860G 9698C 10398G 10550G 11299C 11...
C1H03CaucMT97125Possible 30.70 mixturererunPhylotreeU5a2U5a2C16192T T3197C G9477AT152C A4529T G8251A C11107T T14577G73G 152C 263G 309.1C 315.1C 523del 524del 750G 1438G 2706G 4529T 4769G 7028T 8251A 8860G 11107T 11467G 11719A 12308G 123...
C1A04CaucMT97126PhylotreeU3a1cU3a1cnoneT16342C73G 150T 263G 309.1C 315.1C 750G 1438G 1811G 2294G 2706G 3010A 4703C 4769G 6518T 7028T 8860G 9266A 10506G 11467G 11719A ...
C1B04CaucMT97131PhylotreeJ1c1aJ1c1anoneT11116C C12346T73G 228A 263G 295T 315.1C 462T 482C 489C 750G 1438G 2706G 3010A 3394C 4216C 4769G 7028T 8860G 9635C 10398G 11116C 11251G...
C1C04CaucMT97136Some difficulty with CCCCTCT at position 8280 (heteroplasmic for deletion at 8281-8290?)OKPhylotreeK1a11bK1a11bnoneA16215G A7519-16T 73G 150T 199C 263G 309.1C 315.1C 497T 750G 1189C 1438G 1811G 2706G 3480G 4769G 7028T 7519del 8281del 8282del 8283del...
C1D04CaucMT97139PhylotreeJ2a1a1a2J2a1a1a2noneT6731C73G 150T 152C 195C 215G 263G 295T 310.1T 315.1C 319C 489C 513A 750G 1438G 1850C 2706G 3447G 4216C 4769G 6731C 7028T 7476...
C1E04CaucMT97141GenBank>JQ702482.1X2b+226A16183C T16189C C16223T -309.1C-524.1A -524.2C73G 146C 153G 195C 225A 226C 263G 315.1C 524.1A 524.2C 750G 1438G 1719A 2706G 4769G 6221C 6371T 7028T 8393T 8425G 8860G ...
C1F04CaucMT97145PhylotreeU4a1aU4a1anonenone73G 152C 195C 263G 315.1C 499A 524.1A 524.2C 750G 961C 1438G 1811G 2706G 4646C 4769G 5999C 6047G 7028T 8818T 8860G 11332...
C1G04CaucMT97150GenBank>JQ705315.1H5a1noneT146C -309.2C146C 263G 309.1C 309.2C 315.1C 456T 750G 1438G 4336C 4769G 8860G 9053A 15326G 15833T 16304C 16311C
C1H04CaucMT97152Possible 12% contaminantrerun?PhylotreeHHnonenone263G 309.1C 315.1C 750G 1438G 4769G 8860G 15326G 16519C
C1A05CaucMT97155
C1B05CaucMT97156Many HP in 2-3% range from 9900 through1 to ~700 possible Amplicon1 contaminantrerun?
C1C05CaucMT97158Low coverage from nt 2000 to 9000. No gaps. Possible 5% contaminant in Amplicon 1.Rerun?
C1D05CaucMT97159Good
C1E05CaucPT86478Good
C1F05CaucTT51669Good
C1G05CaucTT51675
C1H05CaucTT51676
C1A06CaucTT51677
C1B06CaucTT51679
C1C06CaucTT51680
C1D06CaucTT51682
C1E06CaucTT51683
C1F06CaucTT51684
C1G06CaucTT51685
C1H06CaucUT58303
Follow-up QC
Analyzed at Q40 and 99% IDAnalyzed at Q35 and 99% ID
C1 plate Amp1 failures
A05MT97155
A07UT58305
B05MT97156
B06TT51679
C01GT38087Min Cov: 11 Max Cov: 6958 Avg Cov: 2410Low coverage from ~ 1,800 to 9,500 (~1000 x) but seems to be complete genome. Position 301-322 appears to be very low coverage. No reads in HV2 C-stretch.
C05MT97158
C09GT36875
C10MT94803some yield
D10MT94807
D11MT94833
E03MT97122
E06TT51683
E07GT38066
E11MT94834
F03MT97123
F12MT94853
G11MT94838
H11MT94839
C1 plate Amp2 failures
A10JT51178
A11MT94827
B09GT36866some yield
C02GT38098Low coverage in Amp2 region, some regions of N's.
D01GT38089Low coverage in Amp2 region, some regions of N's. HV2 C-stretch not covered.
D03MT97121
E01GT38091Low coverage in Amp2 region, one region of N's 13,635 - 13,774. HV2 C-stretch not covered.
F01GT38092Good coverage across genome. May have been quantitation failure. HV2 C-stretch not covered.
G01GT38093Good coverage across genome. May have been quantitation failure. HV2 C-stretch not covered.
G02GT38108
G03MT97124
C1 plate failed both Amp 1&2
G11MT94838
Concordance data
Sample NameSelf ID EthnicityForenSeq-Kidd55 Ancestry SNP ConflictsmitoHg
Peter M. Vallone: Peter M. Vallone:Assigned by Coble or Jodi IrwinGeographical Mito (Coble)Y-HgGeo Y General grouping (de Knijff)refnumberPlatePositionEthnicityNameY-haplogroup (nomenclature Karafet 2008)Haplogroup-E (nomenclature Karafet 2008)Y-haplogroup (nomenclature Jobling 2003)
AF51AAsianD4kAsiaDAsia (mainly Japan, China)X
AF52AAsianD/GAsiaDAsia (mainly Japan, China)X
AF55AAsianD/G (G)
Peter M. Vallone: Peter M. Vallone:Confirmned by Coble and Diegoli - additional mito sequencingAsiaDAsia (mainly Japan, China)X
AF56AAsianD/GAsiaOSouthern part of AsiaX
AF57AAsianF1bAsiaCAsiaX
AF58AAsianM7a1AsiaOSouthern part of AsiaX
AF59AAsianM (M10a)
Peter M. Vallone: Peter M. Vallone:Confirmned by Coble and Diegoli - additional mito sequencingAsiaDAsia (mainly Japan, China)X
AF60AAsianM7a1AsiaOSouthern part of AsiaX
AF61AAsianF1a1bAsiaDAsia (mainly Japan, China)X
AF62AAsianF1aAsiaOSouthern part of AsiaX
AF63AAsianD4a4AsiaOSouthern part of AsiaX
AF64AAsianD4e1a1AsiaOSouthern part of AsiaX
AF65AAsianN (N9)
Peter M. Vallone: Peter M. Vallone:Confirmned by Coble and Diegoli - additional mito sequencingEurasiaOSouthern part of AsiaX
AF66AAsianM35AsiaCAsiaX
AF67AAsianB5b1bAsiaOSouthern part of AsiaX
AF68AAsianD/GAsiaOSouthern part of AsiaX
AF69AAsianF1b1AsiaOSouthern part of AsiaX
AF70AAsianD/GAsiaOSouthern part of AsiaX
AF71AAsianM7b2AsiaOSouthern part of AsiaX
AF72AAsianM35AsiaOSouthern part of AsiaX
AF73AAsianB5bAsiaDAsia (mainly Japan, China)X
AF74AAsianM8a2AsiaOSouthern part of AsiaX
AF75AAsianM9aAsiaOSouthern part of AsiaX
AF76AAsianN9a1AsiaOSouthern part of AsiaX
AF77AAsianAAsiaDAsia (mainly Japan, China)X
AF78AAsianno datano dataERROR:#N/AX
AF79AAsianF1b1AsiaOSouthern part of AsiaX
AF80AAsianD/GAsiaOSouthern part of AsiaX
AF81AAsianB4aAsiaDAsia (mainly Japan, China)X
AF82AAsianD/GAsiaDAsia (mainly Japan, China)X
AF85AAsianD/GAsiaDAsia (mainly Japan, China)X
AF86AAsianF2aAsiaOSouthern part of AsiaX
AF88AAsianD5bAsiaCAsiaX
AF89AAsianD4iAsiaDAsia (mainly Japan, China)X
AF90AAsianB4c1a1aAsiaDAsia (mainly Japan, China)X
AF91AAsianD4c1aincomplete CR dataOSouthern part of AsiaX
AF92AAsianB4c1cAsiaCAsiaX
AF93AAsianD/G (G)
Peter M. Vallone: Peter M. Vallone:Confirmned by Coble and Diegoli - additional mito sequencingAsiaDAsia (mainly Japan, China)X
AF94AAsianB5b1bAsiaOSouthern part of AsiaX
AF95AAsianM7b2AsiaDAsia (mainly Japan, China)X
AF96AAsianD/GAsiaOSouthern part of AsiaX
AF97AAsianB4b1AsiaDAsia (mainly Japan, China)X
AF98AAsianD/GAsiaDAsia (mainly Japan, China)X
BC11352Caucno dataH1Mainly India442Combo1F03CaucBC11352H1n.o.a.H1ok
C51AAsianF1b1AsiaDAsia (mainly Japan, China)X
C52AAsianA5AsiaDAsia (mainly Japan, China)X
C53AAsianM7b2AsiaOSouthern part of AsiaX
GA05070HispA2AmericasQNative American605HispC12HispGA05070Q1an.o.a.Qok
GA05071HispA2AmericasR1b3Mainly western Europe582HispB01HispGA05071R1b1b2n.o.a.R1b3ok
GC03394CaucHEuropeJ2Middle Eastern region281C1H08CaucGC03394J2n.o.a.J2ok
GT36864CaucKEuropeIEurope198C1A09CaucGT36864In.o.a.Iok
GT36866CaucH1aEuropeJ2Middle Eastern region210C1B09CaucGT36866J2n.o.a.J2ok
GT36875CaucTEuropeR1b3Mainly western Europe222C1C09CaucGT3687