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Detailed information for vg0609018460:

Variant ID: vg0609018460 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 9018460
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.76, C: 0.25, others allele: 0.00, population size: 63. )

Flanking Sequence (100 bp) in Reference Genome:


TTGCCTCCTGGGACAAGGATTAATGCACGCACGTAAGGAACGCCCGTTGGGTTATTTCCGGTTGTGACAACTTGACTCTTGGCTAATCAACCCTCTAACA[T/C]
ACTAGATGGATGAACACAAAGCTCAAATGAGTGTGAGAGAGGTGCAAGGGGTGTATGCAATTGAATTGGGTGCCAAGAGAGCCCCCTTGCAGCTGGTGGG

Reverse complement sequence

CCCACCAGCTGCAAGGGGGCTCTCTTGGCACCCAATTCAATTGCATACACCCCTTGCACCTCTCTCACACTCATTTGAGCTTTGTGTTCATCCATCTAGT[A/G]
TGTTAGAGGGTTGATTAGCCAAGAGTCAAGTTGTCACAACCGGAAATAACCCAACGGGCGTTCCTTACGTGCGTGCATTAATCCTTGTCCCAGGAGGCAA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 47.70% 44.00% 3.96% 4.36% NA
All Indica  2759 58.10% 41.00% 0.51% 0.40% NA
All Japonica  1512 39.50% 53.10% 6.81% 0.60% NA
Aus  269 2.60% 7.80% 24.16% 65.43% NA
Indica I  595 56.80% 42.20% 0.84% 0.17% NA
Indica II  465 78.10% 21.70% 0.22% 0.00% NA
Indica III  913 43.20% 56.60% 0.11% 0.11% NA
Indica Intermediate  786 64.60% 33.30% 0.89% 1.15% NA
Temperate Japonica  767 72.80% 19.30% 7.04% 0.91% NA
Tropical Japonica  504 2.80% 93.10% 3.77% 0.40% NA
Japonica Intermediate  241 10.40% 77.20% 12.45% 0.00% NA
VI/Aromatic  96 2.10% 87.50% 4.17% 6.25% NA
Intermediate  90 47.80% 46.70% 1.11% 4.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0609018460 T -> C LOC_Os06g15880.1 splice_region_variant&intron_variant ; LOW silent_mutation Average:34.75; most accessible tissue: Zhenshan97 flag leaf, score: 80.799 N N N N
vg0609018460 T -> C LOC_Os06g15870.1 upstream_gene_variant ; 3845.0bp to feature; MODIFIER silent_mutation Average:34.75; most accessible tissue: Zhenshan97 flag leaf, score: 80.799 N N N N
vg0609018460 T -> C LOC_Os06g15900.1 upstream_gene_variant ; 2954.0bp to feature; MODIFIER silent_mutation Average:34.75; most accessible tissue: Zhenshan97 flag leaf, score: 80.799 N N N N
vg0609018460 T -> C LOC_Os06g15890.1 downstream_gene_variant ; 888.0bp to feature; MODIFIER silent_mutation Average:34.75; most accessible tissue: Zhenshan97 flag leaf, score: 80.799 N N N N
vg0609018460 T -> DEL N N silent_mutation Average:34.75; most accessible tissue: Zhenshan97 flag leaf, score: 80.799 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0609018460 NA 2.71E-14 Grain_length Jap_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0609018460 NA 9.38E-07 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
vg0609018460 NA 8.12E-06 mr1087 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
vg0609018460 NA 3.99E-06 mr1096 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
vg0609018460 NA 1.14E-07 mr1570 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
vg0609018460 NA 4.35E-09 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
vg0609018460 2.44E-06 2.42E-14 mr1087_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
vg0609018460 NA 6.17E-06 mr1091_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
vg0609018460 NA 2.10E-07 mr1096_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
vg0609018460 NA 1.47E-06 mr1341_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
vg0609018460 NA 5.43E-10 mr1530_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
vg0609018460 1.91E-06 5.59E-14 mr1570_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
vg0609018460 NA 2.83E-06 mr1578_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