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Detailed information for vg0622416625:

Variant ID: vg0622416625 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 22416625
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.71, T: 0.30, others allele: 0.00, population size: 200. )

Flanking Sequence (100 bp) in Reference Genome:


TGATCTGAACGAGCATATGCCACATGCTCTTGGGGATCATCGTCAAGGTCGATGTGAGGTCTTACATGAAGATTCTGGTTGTATTCTTCTTCATCGATGA[T/C]
GTTGTCAACTCCGACAATTCGGCGTTTGCCATCCCTCATGATGTGCATCTTCTTGTTTGAAGGGTCTTTTATGTAGAATACCTGCTCGACCTGTTTCGCA

Reverse complement sequence

TGCGAAACAGGTCGAGCAGGTATTCTACATAAAAGACCCTTCAAACAAGAAGATGCACATCATGAGGGATGGCAAACGCCGAATTGTCGGAGTTGACAAC[A/G]
TCATCGATGAAGAAGAATACAACCAGAATCTTCATGTAAGACCTCACATCGACCTTGACGATGATCCCCAAGAGCATGTGGCATATGCTCGTTCAGATCA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 60.10% 35.90% 1.57% 2.45% NA
All Indica  2759 89.20% 4.10% 2.61% 4.06% NA
All Japonica  1512 14.70% 85.10% 0.07% 0.13% NA
Aus  269 29.40% 70.60% 0.00% 0.00% NA
Indica I  595 99.70% 0.30% 0.00% 0.00% NA
Indica II  465 88.20% 3.20% 1.94% 6.67% NA
Indica III  913 82.00% 6.80% 5.70% 5.48% NA
Indica Intermediate  786 90.20% 4.50% 1.40% 3.94% NA
Temperate Japonica  767 2.00% 97.70% 0.13% 0.26% NA
Tropical Japonica  504 36.90% 63.10% 0.00% 0.00% NA
Japonica Intermediate  241 8.70% 91.30% 0.00% 0.00% NA
VI/Aromatic  96 20.80% 79.20% 0.00% 0.00% NA
Intermediate  90 63.30% 33.30% 1.11% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0622416625 T -> C LOC_Os06g37860.1 missense_variant ; p.Ile680Val; MODERATE nonsynonymous_codon ; I680V Average:38.673; most accessible tissue: Zhenshan97 flag leaf, score: 54.545 benign 0.051 TOLERATED 1.00
vg0622416625 T -> DEL LOC_Os06g37860.1 N frameshift_variant Average:38.673; most accessible tissue: Zhenshan97 flag leaf, score: 54.545 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0622416625 NA 4.78E-21 mr1003 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
vg0622416625 NA 2.42E-21 mr1051 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
vg0622416625 NA 1.36E-55 mr1125 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
vg0622416625 NA 4.21E-31 mr1208 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
vg0622416625 NA 8.24E-14 mr1270 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
vg0622416625 NA 1.40E-09 mr1342 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
vg0622416625 NA 3.44E-19 mr1422 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
vg0622416625 NA 5.04E-73 mr1125_2 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
vg0622416625 NA 6.99E-38 mr1208_2 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
vg0622416625 NA 8.12E-24 mr1422_2 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
vg0622416625 NA 9.71E-12 mr1850_2 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
vg0622416625 NA 2.47E-06 mr1850_2 Jap_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