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Detailed information for vg1215515938:

Variant ID: vg1215515938 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 15515938
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, T: 0.02, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:


AGACATAAACATCTTGCAAACTAAGTCATGTGATAATCTTGCTGATTTATTCACAAAATCTCTACCATACTCCACATTCTTTAAATGTGTCGAAGGAATT[G/T]
GTATGAGACGACTTAAAAATATCTTCCTCTGGAAAATAACCTATTTTCGTCATATTATACTCTTTTTCCTTTGTATCAGTTTTACCCTTTAGGTTTTCTC

Reverse complement sequence

GAGAAAACCTAAAGGGTAAAACTGATACAAAGGAAAAAGAGTATAATATGACGAAAATAGGTTATTTTCCAGAGGAAGATATTTTTAAGTCGTCTCATAC[C/A]
AATTCCTTCGACACATTTAAAGAATGTGGAGTATGGTAGAGATTTTGTGAATAAATCAGCAAGATTATCACATGACTTAGTTTGCAAGATGTTTATGTCT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 42.80% 41.90% 0.44% 14.92% NA
All Indica  2759 25.20% 68.90% 0.47% 5.44% NA
All Japonica  1512 70.80% 2.80% 0.26% 26.19% NA
Aus  269 62.80% 1.10% 1.49% 34.57% NA
Indica I  595 7.60% 92.10% 0.34% 0.00% NA
Indica II  465 56.10% 21.70% 1.51% 20.65% NA
Indica III  913 17.40% 80.70% 0.00% 1.86% NA
Indica Intermediate  786 29.40% 65.40% 0.51% 4.71% NA
Temperate Japonica  767 95.30% 1.40% 0.00% 3.26% NA
Tropical Japonica  504 32.90% 2.40% 0.60% 64.09% NA
Japonica Intermediate  241 71.80% 7.90% 0.41% 19.92% NA
VI/Aromatic  96 40.60% 6.20% 0.00% 53.12% NA
Intermediate  90 53.30% 30.00% 0.00% 16.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1215515938 G -> DEL N N silent_mutation Average:12.083; most accessible tissue: Zhenshan97 flag leaf, score: 21.009 N N N N
vg1215515938 G -> T LOC_Os12g26540.1 downstream_gene_variant ; 3776.0bp to feature; MODIFIER silent_mutation Average:12.083; most accessible tissue: Zhenshan97 flag leaf, score: 21.009 N N N N
vg1215515938 G -> T LOC_Os12g26540-LOC_Os12g26560 intergenic_region ; MODIFIER silent_mutation Average:12.083; most accessible tissue: Zhenshan97 flag leaf, score: 21.009 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1215515938 8.61E-06 NA mr1390 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
vg1215515938 3.36E-06 NA mr1490 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
vg1215515938 NA 8.14E-14 mr1531 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
vg1215515938 NA 5.66E-08 mr1860 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
vg1215515938 1.89E-06 NA mr1022_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
vg1215515938 NA 7.99E-09 mr1050_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
vg1215515938 NA 1.59E-06 mr1227_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
vg1215515938 NA 6.63E-07 mr1272_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
vg1215515938 7.02E-06 NA mr1490_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
vg1215515938 NA 2.97E-06 mr1648_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
vg1215515938 NA 1.65E-06 mr1655_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
vg1215515938 NA 6.73E-11 mr1728_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
vg1215515938 NA 1.51E-08 mr1860_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