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Detailed information for vg1007764381:

Variant ID: vg1007764381 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 7764381
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTTGTCACAAAGATGAGACAATATTACATTTGTTTTATGAGTGCAGATTTGCCCGTTTTGTGTGGTGCATTATACAAGTGGCTACAGGACTTTTCCCGCC[A/T]
CGTGGTGTATCCAATATGTTTGGTAATTGGCTACGGGGAATTAAGAAAGACTTGAAGTCACTTATCCTGTTAGAGGCAGCCACTATTTGTTGGTCATTAT

Reverse complement sequence

ATAATGACCAACAAATAGTGGCTGCCTCTAACAGGATAAGTGACTTCAAGTCTTTCTTAATTCCCCGTAGCCAATTACCAAACATATTGGATACACCACG[T/A]
GGCGGGAAAAGTCCTGTAGCCACTTGTATAATGCACCACACAAAACGGGCAAATCTGCACTCATAAAACAAATGTAATATTGTCTCATCTTTGTGACAAA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 27.30% 5.40% 37.07% 30.24% NA
All Indica  2759 11.30% 5.50% 44.58% 38.60% NA
All Japonica  1512 61.40% 0.50% 25.93% 12.17% NA
Aus  269 5.20% 4.80% 30.48% 59.48% NA
Indica I  595 6.60% 11.40% 54.62% 27.39% NA
Indica II  465 11.80% 0.60% 41.94% 45.59% NA
Indica III  913 13.00% 2.40% 41.84% 42.72% NA
Indica Intermediate  786 12.70% 7.40% 41.73% 38.17% NA
Temperate Japonica  767 88.90% 0.00% 7.82% 3.26% NA
Tropical Japonica  504 19.20% 0.60% 57.74% 22.42% NA
Japonica Intermediate  241 61.80% 2.10% 17.01% 19.09% NA
VI/Aromatic  96 7.30% 77.10% 15.62% 0.00% NA
Intermediate  90 30.00% 11.10% 36.67% 22.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1007764381 A -> T LOC_Os10g14814.1 intron_variant ; MODIFIER silent_mutation Average:24.409; most accessible tissue: Zhenshan97 panicle, score: 39.652 N N N N
vg1007764381 A -> DEL N N silent_mutation Average:24.409; most accessible tissue: Zhenshan97 panicle, score: 39.652 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1007764381 6.04E-08 1.19E-08 mr1376 Ind_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
vg1007764381 6.04E-08 1.19E-08 mr1431 Ind_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
vg1007764381 6.93E-06 NA mr1547 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1007764381 3.72E-07 3.42E-07 mr1775 Ind_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
vg1007764381 6.10E-06 1.85E-06 mr1820 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251