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Detailed information for vg0807128963:

Variant ID: vg0807128963 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 7128963
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.65, A: 0.35, others allele: 0.00, population size: 72. )

Flanking Sequence (100 bp) in Reference Genome:


CCCCACGTGGTACGAGAGGCTAGGAGGAAAGCATTTCCCGGGATTCCATGGATTCTCTCCGTTGAGCTCTCTACTTTGCACACTAGGCTGCAAGCTTGAC[A/T]
TGGTGTGAGGAGGCTGGTTTAGCGATGTCTGCCCTGCTAAACCAAGGGAAGGGGCTTCTTTGACATATACCCATGGACAATTCAGGGCATAGTGTCCCTG

Reverse complement sequence

CAGGGACACTATGCCCTGAATTGTCCATGGGTATATGTCAAAGAAGCCCCTTCCCTTGGTTTAGCAGGGCAGACATCGCTAAACCAGCCTCCTCACACCA[T/A]
GTCAAGCTTGCAGCCTAGTGTGCAAAGTAGAGAGCTCAACGGAGAGAATCCATGGAATCCCGGGAAATGCTTTCCTCCTAGCCTCTCGTACCACGTGGGG

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 36.00% 20.20% 30.41% 13.44% NA
All Indica  2759 9.60% 31.90% 41.03% 17.47% NA
All Japonica  1512 89.90% 0.90% 1.59% 7.67% NA
Aus  269 8.60% 13.40% 75.09% 2.97% NA
Indica I  595 22.70% 12.80% 35.97% 28.57% NA
Indica II  465 8.20% 16.60% 49.25% 26.02% NA
Indica III  913 2.10% 53.20% 38.12% 6.57% NA
Indica Intermediate  786 9.30% 30.70% 43.38% 16.67% NA
Temperate Japonica  767 83.40% 0.50% 1.43% 14.60% NA
Tropical Japonica  504 96.40% 1.40% 1.98% 0.20% NA
Japonica Intermediate  241 96.70% 0.80% 1.24% 1.24% NA
VI/Aromatic  96 8.30% 14.60% 54.17% 22.92% NA
Intermediate  90 48.90% 13.30% 30.00% 7.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0807128963 A -> T LOC_Os08g12110.1 missense_variant ; p.Met410Lys; MODERATE nonsynonymous_codon ; M410K Average:16.669; most accessible tissue: Callus, score: 38.257 probably damaging -2.373 TOLERATED 1.00
vg0807128963 A -> DEL LOC_Os08g12110.1 N frameshift_variant Average:16.669; most accessible tissue: Callus, score: 38.257 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0807128963 NA 2.89E-43 mr1136 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
vg0807128963 NA 2.61E-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
vg0807128963 NA 1.38E-45 mr1194 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
vg0807128963 NA 3.95E-35 mr1402 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
vg0807128963 NA 3.10E-20 mr1588 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
vg0807128963 NA 2.27E-20 mr1627 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
vg0807128963 NA 1.11E-08 mr1637 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
vg0807128963 2.84E-06 1.11E-38 mr1828 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
vg0807128963 NA 2.61E-22 mr1888 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
vg0807128963 NA 8.13E-08 mr1004_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
vg0807128963 NA 6.68E-31 mr1105_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
vg0807128963 NA 1.84E-16 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
vg0807128963 NA 1.63E-52 mr1194_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
vg0807128963 NA 2.76E-09 mr1232_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
vg0807128963 NA 7.22E-12 mr1641_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
vg0807128963 NA 2.34E-13 mr1838_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
vg0807128963 NA 3.90E-18 mr1945_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