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Detailed information for vg1212617202:

Variant ID: vg1212617202 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 12617202
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.76, A: 0.25, others allele: 0.00, population size: 227. )

Flanking Sequence (100 bp) in Reference Genome:


TTCCTCCTCTTGCACACAATTAGCGATGAGCTTTTCAAAGTTCCATTTCTCTGGACTTATATTGTAGTTGACAAAAAAGTTGTTAAAGTGCTTTGGCAAT[G/A]
AGACCATAACCAGATGGACCAGAAAGTCATCTGAGATGCCCAAATCTATTGGCTTCAACTTGGAAGCCATGTTGCTCATCCTAAGAATGTGGTCTCTTAC

Reverse complement sequence

GTAAGAGACCACATTCTTAGGATGAGCAACATGGCTTCCAAGTTGAAGCCAATAGATTTGGGCATCTCAGATGACTTTCTGGTCCATCTGGTTATGGTCT[C/T]
ATTGCCAAAGCACTTTAACAACTTTTTTGTCAACTACAATATAAGTCCAGAGAAATGGAACTTTGAAAAGCTCATCGCTAATTGTGTGCAAGAGGAGGAA

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 61.90% 28.30% 0.32% 9.46% NA
All Indica  2759 60.20% 23.50% 0.51% 15.84% NA
All Japonica  1512 56.20% 43.50% 0.07% 0.26% NA
Aus  269 98.90% 1.10% 0.00% 0.00% NA
Indica I  595 53.10% 3.50% 1.18% 42.18% NA
Indica II  465 56.60% 38.10% 0.65% 4.73% NA
Indica III  913 67.90% 24.40% 0.00% 7.67% NA
Indica Intermediate  786 58.70% 28.90% 0.51% 11.96% NA
Temperate Japonica  767 22.60% 77.30% 0.00% 0.13% NA
Tropical Japonica  504 98.00% 1.40% 0.00% 0.60% NA
Japonica Intermediate  241 75.90% 23.70% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 60.00% 33.30% 0.00% 6.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1212617202 G -> DEL LOC_Os12g22350.1 N frameshift_variant Average:30.747; most accessible tissue: Minghui63 flag leaf, score: 64.284 N N N N
vg1212617202 G -> A LOC_Os12g22350.1 missense_variant ; p.Ser24Leu; MODERATE nonsynonymous_codon ; S24L Average:30.747; most accessible tissue: Minghui63 flag leaf, score: 64.284 possibly damaging 1.746 DELETERIOUS 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1212617202 NA 2.37E-08 mr1002 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
vg1212617202 NA 3.59E-11 mr1182 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
vg1212617202 NA 1.79E-06 mr1425 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
vg1212617202 NA 1.77E-06 mr1606 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
vg1212617202 NA 7.52E-06 mr1657 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
vg1212617202 NA 7.54E-08 mr1942 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
vg1212617202 NA 7.69E-11 mr1002_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
vg1212617202 NA 1.50E-06 mr1002_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
vg1212617202 NA 2.29E-08 mr1189_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
vg1212617202 NA 2.38E-08 mr1338_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
vg1212617202 NA 1.57E-08 mr1425_2 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
vg1212617202 NA 7.96E-06 mr1554_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
vg1212617202 NA 1.33E-12 mr1942_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