Search for Variation information by Variation ID:

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

Detailed information for vg1209050414:

Variant ID: vg1209050414 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 9050414
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.67, C: 0.33, others allele: 0.00, population size: 73. )

Flanking Sequence (100 bp) in Reference Genome:


CGATGGCCTAAGAGGTTCCGACCGGGAGCAGTAGAGAAGTACGATGGGAGCACTGACCCAGAAGAATTTCTTCAAGTCTACTCCACAGTACTCTATGCTG[T/C]
CGGATCGGACGACAACGCGTTGGCGAATTATTTGCCAACTGCGTTAAAAGGCTCTGCGCGTTCATGGTTGATGCACCTTCCGCCCTACTCGATTTCTTCG

Reverse complement sequence

CGAAGAAATCGAGTAGGGCGGAAGGTGCATCAACCATGAACGCGCAGAGCCTTTTAACGCAGTTGGCAAATAATTCGCCAACGCGTTGTCGTCCGATCCG[A/G]
CAGCATAGAGTACTGTGGAGTAGACTTGAAGAAATTCTTCTGGGTCAGTGCTCCCATCGTACTTCTCTACTGCTCCCGGTCGGAACCTCTTAGGCCATCG

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 39.40% 35.70% 0.89% 23.99% NA
All Indica  2759 53.80% 6.30% 1.34% 38.56% NA
All Japonica  1512 4.20% 94.30% 0.13% 1.32% NA
Aus  269 80.70% 4.10% 0.00% 15.24% NA
Indica I  595 35.30% 10.30% 1.85% 52.61% NA
Indica II  465 51.40% 7.50% 1.94% 39.14% NA
Indica III  913 65.30% 2.20% 0.77% 31.76% NA
Indica Intermediate  786 55.70% 7.50% 1.27% 35.50% NA
Temperate Japonica  767 5.70% 92.40% 0.26% 1.56% NA
Tropical Japonica  504 3.40% 95.80% 0.00% 0.79% NA
Japonica Intermediate  241 1.20% 97.10% 0.00% 1.66% NA
VI/Aromatic  96 71.90% 22.90% 1.04% 4.17% NA
Intermediate  90 34.40% 57.80% 2.22% 5.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1209050414 T -> C LOC_Os12g15880.1 missense_variant ; p.Val433Ala; MODERATE nonsynonymous_codon ; V433T Average:26.025; most accessible tissue: Minghui63 young leaf, score: 61.887 benign -0.254 TOLERATED 0.11
vg1209050414 T -> C LOC_Os12g15880.1 missense_variant ; p.Val433Ala; MODERATE nonsynonymous_codon ; V433A Average:26.025; most accessible tissue: Minghui63 young leaf, score: 61.887 benign -0.716 TOLERATED 1.00
vg1209050414 T -> DEL LOC_Os12g15880.1 N frameshift_variant Average:26.025; most accessible tissue: Minghui63 young leaf, score: 61.887 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1209050414 NA 1.24E-08 mr1005 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
vg1209050414 2.78E-06 NA mr1016 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
vg1209050414 4.72E-07 1.45E-06 mr1018 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
vg1209050414 2.05E-06 NA mr1132 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
vg1209050414 5.08E-06 NA mr1142 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
vg1209050414 NA 6.36E-19 mr1529 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
vg1209050414 NA 2.76E-20 mr1838 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
vg1209050414 NA 1.60E-08 mr1866 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
vg1209050414 NA 2.97E-51 mr1935 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
vg1209050414 NA 6.80E-07 mr1020_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
vg1209050414 NA 6.80E-15 mr1133_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
vg1209050414 NA 8.50E-17 mr1146_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
vg1209050414 NA 2.67E-15 mr1162_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
vg1209050414 NA 8.49E-11 mr1349_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
vg1209050414 NA 7.62E-14 mr1529_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
vg1209050414 NA 3.46E-45 mr1546_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