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Detailed information for vg1219071207:

Variant ID: vg1219071207 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 19071207
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, G: 0.00, others allele: 0.00, population size: 263. )

Flanking Sequence (100 bp) in Reference Genome:


CATTTTAATTCCAGGAACTGTTGACATGTGTGAGATGACTTCTAAGCACATAAAAGTGTGATATCAAGCAAACAAATGTTAACAAAAAAAAGAATCTTCT[A/G]
AGCACCAAACTACAAAAAATTAACAGATAACAGAAGGTTGCAGTTAATGTCAAAGGTAGTAATGGCTATTCTGTACTTCTATAGATTAGATTACAAAGCA

Reverse complement sequence

TGCTTTGTAATCTAATCTATAGAAGTACAGAATAGCCATTACTACCTTTGACATTAACTGCAACCTTCTGTTATCTGTTAATTTTTTGTAGTTTGGTGCT[T/C]
AGAAGATTCTTTTTTTTGTTAACATTTGTTTGCTTGATATCACACTTTTATGTGCTTAGAAGTCATCTCACACATGTCAACAGTTCCTGGAATTAAAATG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 93.00% 7.00% 0.02% 0.00% NA
All Indica  2759 88.50% 11.40% 0.04% 0.00% NA
All Japonica  1512 99.60% 0.40% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 92.60% 7.40% 0.00% 0.00% NA
Indica II  465 95.30% 4.70% 0.00% 0.00% NA
Indica III  913 82.60% 17.30% 0.11% 0.00% NA
Indica Intermediate  786 88.40% 11.60% 0.00% 0.00% NA
Temperate Japonica  767 99.60% 0.40% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 94.80% 5.20% 0.00% 0.00% NA
Intermediate  90 94.40% 5.60% 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
vg1219071207 A -> G LOC_Os12g31660.1 5_prime_UTR_variant ; 274.0bp to feature; MODIFIER silent_mutation Average:67.903; most accessible tissue: Zhenshan97 panicle, score: 85.254 N N N N
vg1219071207 A -> G LOC_Os12g31650.1 upstream_gene_variant ; 3874.0bp to feature; MODIFIER silent_mutation Average:67.903; most accessible tissue: Zhenshan97 panicle, score: 85.254 N N N N
vg1219071207 A -> G LOC_Os12g31670.1 upstream_gene_variant ; 3919.0bp to feature; MODIFIER silent_mutation Average:67.903; most accessible tissue: Zhenshan97 panicle, score: 85.254 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1219071207 5.20E-07 5.20E-07 mr1682 Ind_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
vg1219071207 NA 6.46E-07 mr1686 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
vg1219071207 1.12E-06 2.41E-06 mr1754 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
vg1219071207 NA 1.75E-08 mr1458_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