AB INITIO GENOME ANNOTATION REPORT · 2019. 12. 18. · AB INITIO GENOME ANNOTATION REPORT Project...
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AB INITIO GENOME ANNOTATION REPORT Project ID : xxxxxxx Species : Chenopodium quinoa Customer : xxxxxxxxxxxxxxxxxxx Company : xxxxxxxxxxxxxxxx ASSESSMENT OF THE INPUT GENOME ASSEMBLY Input assembly Name Assembly size (bp) Input assembly # of scaffolds Input assembly N50 (bp) Quinoa_v1.1.fasta 1,385,456,844 3,486 3,846,917 STATISTICS OF REPEATS MASKED IN THE GENOME Total genome masked 63.46 % Class I TEs repeats 44.69 % Class II TEs repeats 6.23 % Low complexity repeats 0.20 % Simple repeats 1.81 % DE NOVO GENE PREDICTION METRICS Total number of genes Total coding region (bp) Average length of genes (bp) Largest gene (bp) Number of single-exon genes 44,776 57,064,233 1,274 15,933 6,864 AB INITIO GENOME ANNOTATION REPORT PAGE 1
Transcript of AB INITIO GENOME ANNOTATION REPORT · 2019. 12. 18. · AB INITIO GENOME ANNOTATION REPORT Project...
AB INITIO GENOME ANNOTATION REPORT
Project ID : xxxxxxx Species : Chenopodium quinoa
Customer : xxxxxxxxxxxxxxxxxxx Company : xxxxxxxxxxxxxxxx
ASSESSMENT OF THE INPUT GENOME ASSEMBLY
Input assembly Name
Assembly size (bp)
Input assembly # of scaffolds
Input assembly N50 (bp)
Quinoa_v1.1.fasta
1,385,456,844
3,486
3,846,917
STATISTICS OF REPEATS MASKED IN THE GENOME
Total genome masked 63.46 %
Class I TEs repeats 44.69 %
Class II TEs repeats 6.23 %
Low complexity repeats 0.20 %
Simple repeats 1.81 %
DE NOVO GENE PREDICTION METRICS
Total number of genes
Total coding region (bp)
Average length of genes (bp)
Largest gene (bp)
Number of single-exon genes
44,776
57,064,233
1,274
15,933
6,864
AB INITIO GENOME ANNOTATION REPORT PAGE 1
BUSCO ANALYSIS OF PREDICTED GENES
Complete single-copy BUSCOs
Complete duplicated BUSCOs
Fragmented BUSCOs
Missing BUSCOs
Total BUSCO genes searched
906
834
24
26
956
FREQUENCY GRAPH OF AED SCORES
Annotation edit distance (AED) is a general measure of how well the predicted gene is supported by external evidence (UniProt protein and mRNA sequences). AED score ranges from 0 to 1 and a lower score represents more evidence support for the gene. AED is calculated for every gene. The AED cumulative frequency gr aph above provides an overview of the quality of the gene annotation.
AB INITIO GENOME ANNOTATION REPORT PAGE 2
Count Percent
94.80 %
87.20%
2.50%
2.70%
100.00%
LIST OF GENES IDENTIFIED FOR MANUAL CURRATION
Customer genes of interest Matched genes from annotation
Chromatin remodelling protein EBS AUR62017203
Puromycin aminopeptidase AUR62 017183
BHLH - Saponin pathway AUR62017204
Beta Amyrin - Saponin pathway AUR62 025693
Histone acetyltransferase HAC12 AUR62001296
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VISUALISATION OF GENE STRUCTURE FOR AUR62017203
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VISUALISATION OF GENE STRUCTURE FOR AUR62017183
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VISUALISATION OF GENE STRUCTURE FOR AUR62017204
AB INITIO GENOME ANNOTATION REPORT PAGE 6
VISUALISATION OF GENE STRUCTURE FOR AUR62025693
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VISUALISATION OF GENE STRUCTURE FOR AUR62001296
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LIST OF FILES AVAILABLE
1. Soft-masked genome assembly file
2. Genome annotation file in GFF3 format
3. Genes CDS sequences in fasta format
4. Genes peptide sequence in fasta format
5. Gene prediction matrix in text format
6. Bam alignment files from RNAseq and ISOseq data (if data is provided)
AB INITIO GENOME ANNOTATION REPORT PAGE 9
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