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Detailed information for vg1202576537:

Variant ID: vg1202576537 (JBrowse)Variation Type: INDEL
Chromosome: chr12Position: 2576537
Reference Allele: AAlternative Allele: G,ATTTTAAAAAAGCTAGAAAAACACCACCG
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTTTCTGAGAAATCTGTATAATTACACGTGAAAAACATCACTATTTATAAAACAACAGCTTTGAAATAACCATGTGACTCAAAGCGAGAAAAACACCACC[A/G,ATTTTAAAAAAGCTAGAAAAACACCACCG]
TTTATTTTAAAAAAAGCTAGAAAAACACCACCGTTTATTAAAAAAAAAAACTGGTTCGGCACTGTGCAATGCAAAAATGTCCGAATTTAGAAAAAATGCA

Reverse complement sequence

TGCATTTTTTCTAAATTCGGACATTTTTGCATTGCACAGTGCCGAACCAGTTTTTTTTTTTAATAAACGGTGGTGTTTTTCTAGCTTTTTTTAAAATAAA[T/C,CGGTGGTGTTTTTCTAGCTTTTTTAAAAT]
GGTGGTGTTTTTCTCGCTTTGAGTCACATGGTTATTTCAAAGCTGTTGTTTTATAAATAGTGATGTTTTTCACGTGTAATTATACAGATTTCTCAGAAAA

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 87.00% 12.70% 0.17% 0.00% ATTTTAAAAAAGCTAGAAAAACACCACCG: 0.15%
All Indica  2759 85.80% 13.80% 0.18% 0.00% ATTTTAAAAAAGCTAGAAAAACACCACCG: 0.18%
All Japonica  1512 99.80% 0.20% 0.00% 0.00% NA
Aus  269 21.90% 76.60% 0.74% 0.00% ATTTTAAAAAAGCTAGAAAAACACCACCG: 0.74%
Indica I  595 95.60% 4.40% 0.00% 0.00% NA
Indica II  465 86.20% 13.50% 0.00% 0.00% ATTTTAAAAAAGCTAGAAAAACACCACCG: 0.22%
Indica III  913 84.10% 15.80% 0.00% 0.00% ATTTTAAAAAAGCTAGAAAAACACCACCG: 0.11%
Indica Intermediate  786 80.20% 18.80% 0.64% 0.00% ATTTTAAAAAAGCTAGAAAAACACCACCG: 0.38%
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 96.90% 3.10% 0.00% 0.00% NA
Intermediate  90 93.30% 5.60% 1.11% 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
vg1202576537 A -> G LOC_Os12g05609.1 upstream_gene_variant ; 953.0bp to feature; MODIFIER silent_mutation Average:26.527; most accessible tissue: Callus, score: 65.706 N N N N
vg1202576537 A -> G LOC_Os12g05600.1 downstream_gene_variant ; 2622.0bp to feature; MODIFIER silent_mutation Average:26.527; most accessible tissue: Callus, score: 65.706 N N N N
vg1202576537 A -> G LOC_Os12g05609-LOC_Os12g05620 intergenic_region ; MODIFIER silent_mutation Average:26.527; most accessible tissue: Callus, score: 65.706 N N N N
vg1202576537 A -> ATTTTAAAAAAGCTAGAAAAACACCACCG LOC_Os12g05609.1 upstream_gene_variant ; 954.0bp to feature; MODIFIER silent_mutation Average:26.527; most accessible tissue: Callus, score: 65.706 N N N N
vg1202576537 A -> ATTTTAAAAAAGCTAGAAAAACACCACCG LOC_Os12g05600.1 downstream_gene_variant ; 2623.0bp to feature; MODIFIER silent_mutation Average:26.527; most accessible tissue: Callus, score: 65.706 N N N N
vg1202576537 A -> ATTTTAAAAAAGCTAGAAAAACACCACCG LOC_Os12g05609-LOC_Os12g05620 intergenic_region ; MODIFIER silent_mutation Average:26.527; most accessible tissue: Callus, score: 65.706 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1202576537 NA 3.61E-06 mr1071 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
vg1202576537 NA 9.87E-06 mr1125 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
vg1202576537 NA 5.54E-07 mr1286 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
vg1202576537 NA 8.15E-07 mr1438 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
vg1202576537 NA 6.49E-06 mr1467 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
vg1202576537 NA 1.49E-06 mr1523 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
vg1202576537 NA 3.51E-07 mr1574 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
vg1202576537 NA 2.84E-06 mr1665 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