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Detailed information for vg0912250067:

Variant ID: vg0912250067 (JBrowse)Variation Type: INDEL
Chromosome: chr09Position: 12250067
Reference Allele: TAAlternative Allele: AA,TAA,T
Primary Allele: TASecondary Allele: AA

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGAAACAATTTTGGAAAAGAAATGAGGAAGCTAATAGAGGTAGGTGTATAACCGTTGTTCCGTGAGCAATTTGGACAAAAAGAGAAATGGTGCTTTTTTT[TA/AA,TAA,T]
AAAAAAAATTACTGCTAATAGAGGTAGGCTTGATTACTCGCCCGTTGGAGCGAATCAGACATGTCTATTTTTGAGTTTCATTCCAAACTATTTTAAATAA

Reverse complement sequence

TTATTTAAAATAGTTTGGAATGAAACTCAAAAATAGACATGTCTGATTCGCTCCAACGGGCGAGTAATCAAGCCTACCTCTATTAGCAGTAATTTTTTTT[TA/TT,TTA,A]
AAAAAAAGCACCATTTCTCTTTTTGTCCAAATTGCTCACGGAACAACGGTTATACACCTACCTCTATTAGCTTCCTCATTTCTTTTCCAAAATTGTTTCA

Allele Frequencies:

Populations Population SizeFrequency of TA(primary allele) Frequency of AA(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 49.50% 13.10% 21.12% 12.72% TAA: 3.28%; T: 0.23%
All Indica  2759 45.30% 0.90% 32.22% 21.20% T: 0.25%; TAA: 0.14%
All Japonica  1512 52.70% 31.30% 5.82% 0.26% TAA: 9.66%; T: 0.26%
Aus  269 80.30% 16.40% 2.97% 0.37% NA
Indica I  595 28.60% 0.20% 61.68% 9.58% NA
Indica II  465 34.80% 0.60% 21.94% 42.15% TAA: 0.43%
Indica III  913 62.00% 1.30% 19.61% 16.65% T: 0.44%
Indica Intermediate  786 44.80% 1.00% 30.66% 22.90% T: 0.38%; TAA: 0.25%
Temperate Japonica  767 70.10% 9.50% 7.30% 0.26% TAA: 12.39%; T: 0.39%
Tropical Japonica  504 37.70% 55.80% 4.17% 0.00% TAA: 2.18%; T: 0.20%
Japonica Intermediate  241 28.60% 49.40% 4.56% 0.83% TAA: 16.60%
VI/Aromatic  96 34.40% 62.50% 1.04% 1.04% TAA: 1.04%
Intermediate  90 48.90% 22.20% 13.33% 11.11% TAA: 4.44%

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0912250067 TA -> T LOC_Os09g20390.1 upstream_gene_variant ; 1807.0bp to feature; MODIFIER silent_mutation Average:53.763; most accessible tissue: Callus, score: 72.185 N N N N
vg0912250067 TA -> T LOC_Os09g20390.3 upstream_gene_variant ; 1823.0bp to feature; MODIFIER silent_mutation Average:53.763; most accessible tissue: Callus, score: 72.185 N N N N
vg0912250067 TA -> T LOC_Os09g20390.2 upstream_gene_variant ; 1868.0bp to feature; MODIFIER silent_mutation Average:53.763; most accessible tissue: Callus, score: 72.185 N N N N
vg0912250067 TA -> T LOC_Os09g20380-LOC_Os09g20390 intergenic_region ; MODIFIER silent_mutation Average:53.763; most accessible tissue: Callus, score: 72.185 N N N N
vg0912250067 TA -> DEL N N silent_mutation Average:53.763; most accessible tissue: Callus, score: 72.185 N N N N
vg0912250067 TA -> AA LOC_Os09g20390.1 upstream_gene_variant ; 1808.0bp to feature; MODIFIER silent_mutation Average:53.763; most accessible tissue: Callus, score: 72.185 N N N N
vg0912250067 TA -> AA LOC_Os09g20390.3 upstream_gene_variant ; 1824.0bp to feature; MODIFIER silent_mutation Average:53.763; most accessible tissue: Callus, score: 72.185 N N N N
vg0912250067 TA -> AA LOC_Os09g20390.2 upstream_gene_variant ; 1869.0bp to feature; MODIFIER silent_mutation Average:53.763; most accessible tissue: Callus, score: 72.185 N N N N
vg0912250067 TA -> AA LOC_Os09g20380-LOC_Os09g20390 intergenic_region ; MODIFIER silent_mutation Average:53.763; most accessible tissue: Callus, score: 72.185 N N N N
vg0912250067 TA -> TAA LOC_Os09g20390.1 upstream_gene_variant ; 1806.0bp to feature; MODIFIER silent_mutation Average:53.763; most accessible tissue: Callus, score: 72.185 N N N N
vg0912250067 TA -> TAA LOC_Os09g20390.3 upstream_gene_variant ; 1822.0bp to feature; MODIFIER silent_mutation Average:53.763; most accessible tissue: Callus, score: 72.185 N N N N
vg0912250067 TA -> TAA LOC_Os09g20390.2 upstream_gene_variant ; 1867.0bp to feature; MODIFIER silent_mutation Average:53.763; most accessible tissue: Callus, score: 72.185 N N N N
vg0912250067 TA -> TAA LOC_Os09g20380-LOC_Os09g20390 intergenic_region ; MODIFIER silent_mutation Average:53.763; most accessible tissue: Callus, score: 72.185 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0912250067 2.53E-07 4.70E-09 mr1159 Jap_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
vg0912250067 NA 2.94E-06 mr1342 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