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Detailed information for vg1009252761:

Variant ID: vg1009252761 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 9252761
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 318. )

Flanking Sequence (100 bp) in Reference Genome:


TTCACTGTGTACCTCATGGATGACACTCCTAAGTCAATTTCAGAAGCATATGCATCTCCTGATGCAGACTACTGGAAGGAGGCTGTCCGTAGTGAAATGG[A/T]
TTCCATTATCACTAACGGGACTTGGGAGGTGACAGAGCGACCCTGTGGGTGTAAACCTGTGGGGTGCAAGTGGGTGTTCAAGAAGAAGCTTAGGCCTGAC

Reverse complement sequence

GTCAGGCCTAAGCTTCTTCTTGAACACCCACTTGCACCCCACAGGTTTACACCCACAGGGTCGCTCTGTCACCTCCCAAGTCCCGTTAGTGATAATGGAA[T/A]
CCATTTCACTACGGACAGCCTCCTTCCAGTAGTCTGCATCAGGAGATGCATATGCTTCTGAAATTGACTTAGGAGTGTCATCCATGAGGTACACAGTGAA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 75.50% 24.40% 0.15% 0.00% NA
All Indica  2759 60.70% 39.00% 0.25% 0.00% NA
All Japonica  1512 96.50% 3.50% 0.00% 0.00% NA
Aus  269 98.10% 1.90% 0.00% 0.00% NA
Indica I  595 74.50% 25.20% 0.34% 0.00% NA
Indica II  465 41.30% 58.50% 0.22% 0.00% NA
Indica III  913 65.00% 34.80% 0.22% 0.00% NA
Indica Intermediate  786 57.00% 42.70% 0.25% 0.00% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 90.50% 9.50% 0.00% 0.00% NA
Japonica Intermediate  241 98.80% 1.20% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 80.00% 20.00% 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
vg1009252761 A -> T LOC_Os10g18210.1 missense_variant ; p.Asp415Val; MODERATE nonsynonymous_codon ; D415V Average:29.945; most accessible tissue: Minghui63 young leaf, score: 57.221 probably damaging 2.201 DELETERIOUS 0.00

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1009252761 1.66E-06 3.32E-11 mr1053 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
vg1009252761 1.77E-06 1.89E-07 mr1053 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
vg1009252761 7.01E-07 NA mr1070 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
vg1009252761 3.10E-07 7.71E-07 mr1070 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
vg1009252761 4.97E-06 1.79E-06 mr1128 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
vg1009252761 3.63E-06 3.35E-06 mr1147 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
vg1009252761 NA 1.07E-07 mr1709 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
vg1009252761 NA 5.15E-08 mr1027_2 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
vg1009252761 NA 1.07E-08 mr1053_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
vg1009252761 NA 1.29E-06 mr1053_2 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
vg1009252761 NA 2.77E-06 mr1250_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