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Detailed information for vg0817943381:

Variant ID: vg0817943381 (JBrowse)Variation Type: INDEL
Chromosome: chr08Position: 17943381
Reference Allele: CTAAlternative Allele: ATA,C
Primary Allele: CTASecondary Allele: ATA

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTCGACTAGCTCATCTGGAATTTTGTCATCTATTTCATGGAGCCTATCTCTAATAGGGACCACCTGCGATTATTCCAGGCGGTCTATTTATGTGGTCCGC[CTA/ATA,C]
TGAAGCTCCATCTTCGCAGGCGCCCATTTTTTGCCACCTGCAAAATTCATTCACGGCAACACCATTTACCGCCTATAAAAATCTGGCCGACTATATAGTC

Reverse complement sequence

GACTATATAGTCGGCCAGATTTTTATAGGCGGTAAATGGTGTTGCCGTGAATGAATTTTGCAGGTGGCAAAAAATGGGCGCCTGCGAAGATGGAGCTTCA[TAG/TAT,G]
GCGGACCACATAAATAGACCGCCTGGAATAATCGCAGGTGGTCCCTATTAGAGATAGGCTCCATGAAATAGATGACAAAATTCCAGATGAGCTAGTCGAA

Allele Frequencies:

Populations Population SizeFrequency of CTA(primary allele) Frequency of ATA(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 85.70% 6.90% 0.59% 6.81% C: 0.02%
All Indica  2759 87.50% 0.10% 0.94% 11.38% C: 0.04%
All Japonica  1512 84.70% 14.90% 0.07% 0.33% NA
Aus  269 98.50% 1.50% 0.00% 0.00% NA
Indica I  595 93.60% 0.00% 0.67% 5.71% NA
Indica II  465 98.90% 0.00% 0.22% 0.86% NA
Indica III  913 82.30% 0.20% 1.31% 16.10% C: 0.11%
Indica Intermediate  786 82.20% 0.30% 1.15% 16.41% NA
Temperate Japonica  767 88.00% 11.70% 0.00% 0.26% NA
Tropical Japonica  504 89.90% 9.50% 0.00% 0.60% NA
Japonica Intermediate  241 63.50% 36.10% 0.41% 0.00% NA
VI/Aromatic  96 16.70% 80.20% 1.04% 2.08% NA
Intermediate  90 83.30% 15.60% 0.00% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0817943381 CTA -> C LOC_Os08g29250.1 upstream_gene_variant ; 4720.0bp to feature; MODIFIER silent_mutation Average:46.721; most accessible tissue: Zhenshan97 young leaf, score: 64.747 N N N N
vg0817943381 CTA -> C LOC_Os08g29280.1 upstream_gene_variant ; 3071.0bp to feature; MODIFIER silent_mutation Average:46.721; most accessible tissue: Zhenshan97 young leaf, score: 64.747 N N N N
vg0817943381 CTA -> C LOC_Os08g29260.1 downstream_gene_variant ; 1190.0bp to feature; MODIFIER silent_mutation Average:46.721; most accessible tissue: Zhenshan97 young leaf, score: 64.747 N N N N
vg0817943381 CTA -> C LOC_Os08g29270.1 intron_variant ; MODIFIER silent_mutation Average:46.721; most accessible tissue: Zhenshan97 young leaf, score: 64.747 N N N N
vg0817943381 CTA -> ATA LOC_Os08g29250.1 upstream_gene_variant ; 4719.0bp to feature; MODIFIER silent_mutation Average:46.721; most accessible tissue: Zhenshan97 young leaf, score: 64.747 N N N N
vg0817943381 CTA -> ATA LOC_Os08g29280.1 upstream_gene_variant ; 3072.0bp to feature; MODIFIER silent_mutation Average:46.721; most accessible tissue: Zhenshan97 young leaf, score: 64.747 N N N N
vg0817943381 CTA -> ATA LOC_Os08g29260.1 downstream_gene_variant ; 1189.0bp to feature; MODIFIER silent_mutation Average:46.721; most accessible tissue: Zhenshan97 young leaf, score: 64.747 N N N N
vg0817943381 CTA -> ATA LOC_Os08g29270.1 intron_variant ; MODIFIER silent_mutation Average:46.721; most accessible tissue: Zhenshan97 young leaf, score: 64.747 N N N N
vg0817943381 CTA -> DEL N N silent_mutation Average:46.721; most accessible tissue: Zhenshan97 young leaf, score: 64.747 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0817943381 2.20E-06 NA mr1080 All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251