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Detailed information for vg0315006440:

Variant ID: vg0315006440 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 15006440
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.96, A: 0.03, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:


GTGCTTGACGTGGAAATGAAAACTGCACTCTGAAATGCACCTTTTGAATCCTAACCGAAAGAGTAAAGTGTTTGACTATAGGGGCATATATCTTGGAGAC[G/A]
TTCGCTCATGATATGAGGATCAGTAGCTCTTGATATAAATTGACTGTTGTTTCAAACGTGGTTTTTTATTTGATGCCTTAGATTTTCGTACATTTACCTG

Reverse complement sequence

CAGGTAAATGTACGAAAATCTAAGGCATCAAATAAAAAACCACGTTTGAAACAACAGTCAATTTATATCAAGAGCTACTGATCCTCATATCATGAGCGAA[C/T]
GTCTCCAAGATATATGCCCCTATAGTCAAACACTTTACTCTTTCGGTTAGGATTCAAAAGGTGCATTTCAGAGTGCAGTTTTCATTTCCACGTCAAGCAC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 59.20% 37.20% 2.56% 1.04% NA
All Indica  2759 71.70% 27.80% 0.54% 0.00% NA
All Japonica  1512 43.90% 46.30% 6.55% 3.24% NA
Aus  269 4.80% 93.30% 1.86% 0.00% NA
Indica I  595 47.10% 52.30% 0.67% 0.00% NA
Indica II  465 52.70% 46.00% 1.29% 0.00% NA
Indica III  913 89.70% 10.00% 0.33% 0.00% NA
Indica Intermediate  786 80.70% 19.10% 0.25% 0.00% NA
Temperate Japonica  767 18.00% 64.70% 11.86% 5.48% NA
Tropical Japonica  504 65.30% 32.90% 0.60% 1.19% NA
Japonica Intermediate  241 81.70% 15.80% 2.07% 0.41% NA
VI/Aromatic  96 92.70% 7.30% 0.00% 0.00% NA
Intermediate  90 57.80% 40.00% 2.22% 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
vg0315006440 G -> A LOC_Os03g26220.1 upstream_gene_variant ; 1877.0bp to feature; MODIFIER silent_mutation Average:58.489; most accessible tissue: Callus, score: 82.42 N N N N
vg0315006440 G -> A LOC_Os03g26250.1 upstream_gene_variant ; 4722.0bp to feature; MODIFIER silent_mutation Average:58.489; most accessible tissue: Callus, score: 82.42 N N N N
vg0315006440 G -> A LOC_Os03g26210.1 downstream_gene_variant ; 4235.0bp to feature; MODIFIER silent_mutation Average:58.489; most accessible tissue: Callus, score: 82.42 N N N N
vg0315006440 G -> A LOC_Os03g26240.1 downstream_gene_variant ; 2315.0bp to feature; MODIFIER silent_mutation Average:58.489; most accessible tissue: Callus, score: 82.42 N N N N
vg0315006440 G -> A LOC_Os03g26210.3 downstream_gene_variant ; 4235.0bp to feature; MODIFIER silent_mutation Average:58.489; most accessible tissue: Callus, score: 82.42 N N N N
vg0315006440 G -> A LOC_Os03g26210.2 downstream_gene_variant ; 4235.0bp to feature; MODIFIER silent_mutation Average:58.489; most accessible tissue: Callus, score: 82.42 N N N N
vg0315006440 G -> A LOC_Os03g26229.1 intron_variant ; MODIFIER silent_mutation Average:58.489; most accessible tissue: Callus, score: 82.42 N N N N
vg0315006440 G -> DEL N N silent_mutation Average:58.489; most accessible tissue: Callus, score: 82.42 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0315006440 2.06E-06 2.06E-06 mr1030 Jap_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
vg0315006440 6.87E-06 3.62E-09 mr1045 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
vg0315006440 2.30E-06 2.30E-06 mr1053 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
vg0315006440 NA 1.19E-06 mr1072 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
vg0315006440 NA 9.72E-06 mr1077 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
vg0315006440 NA 1.73E-07 mr1164 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
vg0315006440 NA 3.71E-06 mr1170 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
vg0315006440 NA 2.63E-06 mr1179 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
vg0315006440 NA 1.19E-07 mr1192 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
vg0315006440 NA 1.27E-06 mr1202 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
vg0315006440 NA 9.58E-06 mr1205 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
vg0315006440 NA 6.29E-07 mr1236 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
vg0315006440 NA 7.55E-07 mr1237 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
vg0315006440 NA 3.70E-06 mr1263 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
vg0315006440 NA 4.37E-08 mr1280 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
vg0315006440 NA 6.03E-07 mr1289 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
vg0315006440 NA 9.61E-06 mr1318 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
vg0315006440 NA 1.65E-06 mr1330 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
vg0315006440 NA 1.29E-06 mr1359 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
vg0315006440 NA 4.12E-06 mr1380 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
vg0315006440 2.38E-06 2.38E-06 mr1412 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
vg0315006440 5.94E-06 5.94E-06 mr1430 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
vg0315006440 NA 3.70E-06 mr1451 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
vg0315006440 NA 5.44E-09 mr1521 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
vg0315006440 9.23E-07 9.23E-07 mr1556 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
vg0315006440 NA 2.36E-07 mr1576 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
vg0315006440 8.10E-06 8.10E-06 mr1634 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
vg0315006440 NA 1.68E-06 mr1668 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
vg0315006440 1.37E-06 2.16E-07 mr1683 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
vg0315006440 NA 2.23E-07 mr1723 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
vg0315006440 NA 5.15E-10 mr1729 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
vg0315006440 NA 8.94E-07 mr1741 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
vg0315006440 NA 1.55E-07 mr1788 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
vg0315006440 NA 8.55E-06 mr1809 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
vg0315006440 6.85E-06 6.85E-06 mr1820 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
vg0315006440 NA 1.24E-07 mr1844 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
vg0315006440 NA 4.00E-06 mr1906 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