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Detailed information for vg1119474674:

Variant ID: vg1119474674 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 19474674
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:


GTTCTGGGTTCGACTCTCATGGGTGGGAACGAATTAAATATTGTGCTTTCAATGATAGGCGATGTACCCGTTGACAGCGAGACACCTATGGTGGCTTCGT[C/T]
AATCTCAATTTTTTAGACTTTTTGGTGTTTGAATCTCCTGAAAATGAAGATGGAGATAAAGATTAAGTGTTCCACATAAAACGAGATGGTAATAATGTTT

Reverse complement sequence

AAACATTATTACCATCTCGTTTTATGTGGAACACTTAATCTTTATCTCCATCTTCATTTTCAGGAGATTCAAACACCAAAAAGTCTAAAAAATTGAGATT[G/A]
ACGAAGCCACCATAGGTGTCTCGCTGTCAACGGGTACATCGCCTATCATTGAAAGCACAATATTTAATTCGTTCCCACCCATGAGAGTCGAACCCAGAAC

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 81.00% 18.60% 0.44% 0.00% NA
All Indica  2759 90.40% 9.50% 0.07% 0.00% NA
All Japonica  1512 70.40% 28.30% 1.26% 0.00% NA
Aus  269 38.70% 61.30% 0.00% 0.00% NA
Indica I  595 93.80% 6.20% 0.00% 0.00% NA
Indica II  465 75.50% 24.50% 0.00% 0.00% NA
Indica III  913 96.70% 3.30% 0.00% 0.00% NA
Indica Intermediate  786 89.30% 10.40% 0.25% 0.00% NA
Temperate Japonica  767 90.20% 9.10% 0.65% 0.00% NA
Tropical Japonica  504 41.90% 56.20% 1.98% 0.00% NA
Japonica Intermediate  241 67.20% 31.10% 1.66% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 74.40% 25.60% 0.00% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1119474674 C -> T LOC_Os11g32950.1 upstream_gene_variant ; 1063.0bp to feature; MODIFIER silent_mutation Average:49.486; most accessible tissue: Zhenshan97 panicle, score: 80.486 N N N N
vg1119474674 C -> T LOC_Os11g32940-LOC_Os11g32950 intergenic_region ; MODIFIER silent_mutation Average:49.486; most accessible tissue: Zhenshan97 panicle, score: 80.486 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1119474674 NA 4.22E-06 mr1502 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
vg1119474674 NA 6.09E-06 mr1502 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
vg1119474674 NA 1.70E-06 mr1543 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
vg1119474674 NA 2.01E-09 mr1648 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
vg1119474674 7.44E-07 NA mr1871 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
vg1119474674 1.10E-06 5.60E-10 mr1871 Jap_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
vg1119474674 5.44E-08 NA mr1871_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
vg1119474674 NA 2.66E-08 mr1871_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