Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923).

Detailed information for vg1115688831:

Variant ID: vg1115688831 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 15688831
Reference Allele: AAlternative Allele: C
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 111. )

Flanking Sequence (100 bp) in Reference Genome:


TATAATCCTTCTCATATCCCTTGGATTCTTCATAAAGAAGATCCTCCGTTGGTTTCTATAATGCCTCTTAGTTGTCTAATCCCCGTGCTGTACCCATAAG[A/C]
ACCTCTGGTTTAGCGTGGTGCATCATATCTTCTAGACTGAATTCTGCCTCAAAATCGTCACTACTAGTCGAACCATCTTCATCCATTCTTTCAAGGGCCA

Reverse complement sequence

TGGCCCTTGAAAGAATGGATGAAGATGGTTCGACTAGTAGTGACGATTTTGAGGCAGAATTCAGTCTAGAAGATATGATGCACCACGCTAAACCAGAGGT[T/G]
CTTATGGGTACAGCACGGGGATTAGACAACTAAGAGGCATTATAGAAACCAACGGAGGATCTTCTTTATGAAGAATCCAAGGGATATGAGAAGGATTATA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 24.10% 9.40% 2.09% 64.43% NA
All Indica  2759 1.90% 0.50% 0.65% 96.92% NA
All Japonica  1512 63.90% 27.90% 5.16% 3.04% NA
Aus  269 0.40% 0.00% 0.37% 99.26% NA
Indica I  595 2.50% 0.50% 0.67% 96.30% NA
Indica II  465 0.20% 0.60% 0.22% 98.92% NA
Indica III  913 0.50% 0.20% 0.55% 98.69% NA
Indica Intermediate  786 4.10% 0.80% 1.02% 94.15% NA
Temperate Japonica  767 41.20% 49.20% 6.91% 2.74% NA
Tropical Japonica  504 91.50% 2.20% 2.58% 3.77% NA
Japonica Intermediate  241 78.40% 14.10% 4.98% 2.49% NA
VI/Aromatic  96 91.70% 1.00% 0.00% 7.29% NA
Intermediate  90 34.40% 6.70% 2.22% 56.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1115688831 A -> DEL N N silent_mutation Average:8.904; most accessible tissue: Callus, score: 34.974 N N N N
vg1115688831 A -> C LOC_Os11g27264.1 intron_variant ; MODIFIER silent_mutation Average:8.904; most accessible tissue: Callus, score: 34.974 N N N N
vg1115688831 A -> C LOC_Os11g27264.2 intron_variant ; MODIFIER silent_mutation Average:8.904; most accessible tissue: Callus, score: 34.974 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1115688831 NA 3.26E-09 mr1137 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
vg1115688831 NA 1.11E-07 mr1162 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
vg1115688831 NA 1.73E-06 mr1162 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
vg1115688831 NA 1.02E-07 mr1163 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
vg1115688831 NA 5.00E-06 mr1164 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
vg1115688831 NA 7.44E-07 mr1202 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
vg1115688831 NA 9.18E-06 mr1271 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
vg1115688831 NA 3.38E-07 mr1271 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
vg1115688831 NA 8.30E-06 mr1359 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
vg1115688831 NA 4.67E-06 mr1380 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
vg1115688831 NA 3.47E-06 mr1521 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
vg1115688831 NA 5.27E-06 mr1555 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
vg1115688831 NA 4.11E-07 mr1576 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
vg1115688831 NA 9.33E-06 mr1576 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
vg1115688831 NA 3.77E-09 mr1617 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
vg1115688831 1.36E-06 NA mr1789 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
vg1115688831 NA 1.01E-07 mr1804 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
vg1115688831 NA 4.12E-09 mr1137_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
vg1115688831 NA 2.28E-09 mr1576_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
vg1115688831 NA 5.84E-07 mr1576_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
vg1115688831 NA 1.11E-06 mr1617_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