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Detailed information for vg0222144498:

Variant ID: vg0222144498 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 22144498
Reference Allele: TAlternative Allele: G
Primary Allele: TSecondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 286. )

Flanking Sequence (100 bp) in Reference Genome:


TTTCATAAAAGTGCAACAAAGGTAATCTGTAAAAAAAAAAAATCACAAGTGACTGACAAACACATACAGCACAATTTGGTGTCAACCAACCACCACCGAT[T/G]
GAAACTCCTTTTAGTAAAAAAAAAAACATGGCACGAGTTTGAGCAATGGTGCAAGAGCAAAGATTGGGATTCAGTTTGCATCGCTGAATGAATCGCCAAC

Reverse complement sequence

GTTGGCGATTCATTCAGCGATGCAAACTGAATCCCAATCTTTGCTCTTGCACCATTGCTCAAACTCGTGCCATGTTTTTTTTTTTACTAAAAGGAGTTTC[A/C]
ATCGGTGGTGGTTGGTTGACACCAAATTGTGCTGTATGTGTTTGTCAGTCACTTGTGATTTTTTTTTTTTACAGATTACCTTTGTTGCACTTTTATGAAA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 91.10% 8.70% 0.21% 0.00% NA
All Indica  2759 95.70% 4.20% 0.07% 0.00% NA
All Japonica  1512 84.40% 15.10% 0.53% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 98.80% 1.00% 0.17% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 93.20% 6.70% 0.11% 0.00% NA
Indica Intermediate  786 93.80% 6.20% 0.00% 0.00% NA
Temperate Japonica  767 91.00% 8.70% 0.26% 0.00% NA
Tropical Japonica  504 90.10% 9.70% 0.20% 0.00% NA
Japonica Intermediate  241 51.50% 46.50% 2.07% 0.00% NA
VI/Aromatic  96 40.60% 59.40% 0.00% 0.00% NA
Intermediate  90 91.10% 8.90% 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
vg0222144498 T -> G LOC_Os02g36680.1 upstream_gene_variant ; 2502.0bp to feature; MODIFIER silent_mutation Average:43.509; most accessible tissue: Callus, score: 74.466 N N N N
vg0222144498 T -> G LOC_Os02g36700.1 downstream_gene_variant ; 1922.0bp to feature; MODIFIER silent_mutation Average:43.509; most accessible tissue: Callus, score: 74.466 N N N N
vg0222144498 T -> G LOC_Os02g36690.1 intron_variant ; MODIFIER silent_mutation Average:43.509; most accessible tissue: Callus, score: 74.466 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0222144498 NA 2.40E-06 mr1057 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
vg0222144498 NA 6.55E-06 mr1913 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
vg0222144498 NA 6.59E-07 mr1057_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
vg0222144498 NA 4.32E-06 mr1113_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
vg0222144498 NA 1.81E-06 mr1118_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
vg0222144498 NA 8.75E-06 mr1123_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
vg0222144498 NA 4.04E-06 mr1240_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
vg0222144498 8.35E-08 NA mr1334_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
vg0222144498 NA 9.65E-07 mr1496_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
vg0222144498 NA 4.76E-07 mr1691_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
vg0222144498 1.47E-06 NA mr1991_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