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Detailed information for vg0412479470:

Variant ID: vg0412479470 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 12479470
Reference Allele: TAlternative Allele: A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.94, A: 0.05, others allele: 0.00, population size: 127. )

Flanking Sequence (100 bp) in Reference Genome:


CGGATCTAAATCTCCGACAACGAAGATGGCTGGAACTAATCAAAGATTATGACATGAGCATTCACTACCATCCGGGTAAAGCCAATGTGGTGGCAGATGC[T/A]
TTAAGCAGGAAAAGCTACTGCAATGCCCTATGCACCGAGGACATGTGTGAAGAATTGCAGCAGGAGCTTGAACGTCTCAACGTGGGAATCGTTGAACACA

Reverse complement sequence

TGTGTTCAACGATTCCCACGTTGAGACGTTCAAGCTCCTGCTGCAATTCTTCACACATGTCCTCGGTGCATAGGGCATTGCAGTAGCTTTTCCTGCTTAA[A/T]
GCATCTGCCACCACATTGGCTTTACCCGGATGGTAGTGAATGCTCATGTCATAATCTTTGATTAGTTCCAGCCATCTTCGTTGTCGGAGATTTAGATCCG

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 49.70% 36.70% 6.07% 7.49% NA
All Indica  2759 23.60% 56.90% 10.04% 9.42% NA
All Japonica  1512 99.20% 0.80% 0.00% 0.00% NA
Aus  269 20.10% 45.40% 1.86% 32.71% NA
Indica I  595 47.40% 31.10% 10.92% 10.59% NA
Indica II  465 23.90% 69.90% 3.66% 2.58% NA
Indica III  913 6.00% 67.50% 14.57% 11.94% NA
Indica Intermediate  786 26.00% 56.50% 7.89% 9.67% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 99.00% 1.00% 0.00% 0.00% NA
Japonica Intermediate  241 97.90% 2.10% 0.00% 0.00% NA
VI/Aromatic  96 92.70% 5.20% 2.08% 0.00% NA
Intermediate  90 61.10% 28.90% 3.33% 6.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0412479470 T -> DEL LOC_Os04g22030.1 N frameshift_variant Average:35.133; most accessible tissue: Minghui63 young leaf, score: 47.146 N N N N
vg0412479470 T -> A LOC_Os04g22030.1 synonymous_variant ; p.Ala648Ala; LOW synonymous_codon Average:35.133; most accessible tissue: Minghui63 young leaf, score: 47.146 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0412479470 9.16E-07 NA mr1071 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
vg0412479470 2.89E-07 1.39E-84 mr1080 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
vg0412479470 7.09E-06 NA mr1140 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
vg0412479470 NA 8.41E-28 mr1148 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
vg0412479470 4.50E-06 NA mr1203 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
vg0412479470 NA 1.36E-34 mr1350 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
vg0412479470 4.25E-06 3.97E-78 mr1613 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
vg0412479470 4.29E-06 NA mr1618 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
vg0412479470 NA 1.72E-26 mr1632 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
vg0412479470 NA 8.06E-52 mr1795 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
vg0412479470 NA 7.35E-12 mr1940 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
vg0412479470 NA 3.53E-61 mr1962 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
vg0412479470 6.24E-08 1.38E-104 mr1071_2 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
vg0412479470 5.60E-08 2.27E-106 mr1080_2 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
vg0412479470 1.28E-06 6.25E-103 mr1100_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
vg0412479470 NA 1.23E-14 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
vg0412479470 4.76E-07 NA mr1203_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
vg0412479470 4.14E-07 2.76E-120 mr1613_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
vg0412479470 3.96E-07 1.10E-101 mr1619_2 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
vg0412479470 9.23E-06 NA mr1962_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