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Detailed information for vg1108349674:

Variant ID: vg1108349674 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 8349674
Reference Allele: GAlternative Allele: T,C
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.56, G: 0.44, others allele: 0.00, population size: 50. )

Flanking Sequence (100 bp) in Reference Genome:


ATTCCTTTCGATGAAGGGGGGAGCTGTTCGACTCCACCCCTGGTCTCGTTGTGACCTGGACTTGGTGTAGGAGTGTAGCCAGGGGTGTCGACGCGGTTTT[G/T,C]
GACTGCCTCATCTGCGGCCTTTTCGACCACGGCCTCCGCCTCCTCTTCCTCCTCCCCTTCTTCATCGCCGTCACGCTCTTCGACGTCGTCCTTGTCATTA

Reverse complement sequence

TAATGACAAGGACGACGTCGAAGAGCGTGACGGCGATGAAGAAGGGGAGGAGGAAGAGGAGGCGGAGGCCGTGGTCGAAAAGGCCGCAGATGAGGCAGTC[C/A,G]
AAAACCGCGTCGACACCCCTGGCTACACTCCTACACCAAGTCCAGGTCACAACGAGACCAGGGGTGGAGTCGAACAGCTCCCCCCTTCATCGAAAGGAAT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 40.00% 25.00% 12.55% 22.18% C: 0.34%
All Indica  2759 7.30% 41.20% 17.72% 33.71% C: 0.04%
All Japonica  1512 90.10% 1.60% 1.72% 6.22% C: 0.33%
Aus  269 72.90% 1.10% 23.42% 2.60% NA
Indica I  595 12.90% 63.40% 7.56% 16.13% NA
Indica II  465 5.20% 19.60% 19.14% 56.13% NA
Indica III  913 1.60% 43.00% 21.25% 34.06% NA
Indica Intermediate  786 10.90% 35.10% 20.48% 33.33% C: 0.13%
Temperate Japonica  767 97.90% 1.70% 0.26% 0.13% NA
Tropical Japonica  504 81.00% 1.60% 1.19% 16.07% C: 0.20%
Japonica Intermediate  241 84.60% 1.20% 7.47% 4.98% C: 1.66%
VI/Aromatic  96 89.60% 0.00% 1.04% 1.04% C: 8.33%
Intermediate  90 46.70% 17.80% 15.56% 17.78% C: 2.22%

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1108349674 G -> T LOC_Os11g14840.1 missense_variant ; p.Gln327Lys; MODERATE nonsynonymous_codon ; Q327K Average:16.848; most accessible tissue: Callus, score: 26.589 benign -1.217 TOLERATED 0.15
vg1108349674 G -> DEL LOC_Os11g14840.1 N frameshift_variant Average:16.848; most accessible tissue: Callus, score: 26.589 N N N N
vg1108349674 G -> C LOC_Os11g14840.1 missense_variant ; p.Gln327Glu; MODERATE nonsynonymous_codon ; Q327E Average:16.848; most accessible tissue: Callus, score: 26.589 possibly damaging -1.698 TOLERATED 1.00

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1108349674 2.60E-06 NA mr1089 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
vg1108349674 9.11E-06 NA mr1093 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
vg1108349674 NA 4.60E-34 mr1129 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
vg1108349674 NA 8.02E-13 mr1183 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
vg1108349674 NA 4.13E-19 mr1255 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
vg1108349674 NA 1.57E-10 mr1720 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
vg1108349674 NA 3.52E-49 mr1063_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
vg1108349674 NA 1.09E-16 mr1180_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
vg1108349674 NA 1.18E-22 mr1183_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
vg1108349674 NA 5.85E-09 mr1198_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
vg1108349674 NA 3.19E-11 mr1228_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
vg1108349674 NA 2.64E-21 mr1401_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
vg1108349674 NA 7.73E-09 mr1751_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
vg1108349674 NA 1.22E-07 mr1885_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
vg1108349674 NA 1.04E-24 mr1943_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