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Detailed information for vg0136265772:

Variant ID: vg0136265772 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 36265772
Reference Allele: CAlternative Allele: T,A
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATATGAAAACGAATATGATAAAGCTAGTTTCCGTCCGTTTCCGATCCGTTTTCATTCCTAGTCACTACTGCAAATCGTCATGTTTTACATATTTTTGTTG[C/T,A]
TGGTGGAATGGATTTGGCCATCATCTATGAGAAAAATGTCTACATGCTAGCTACCTTCATCAGCTCCGTTGGAAATGCTTTGAGATGGTGCTGATTTGCT

Reverse complement sequence

AGCAAATCAGCACCATCTCAAAGCATTTCCAACGGAGCTGATGAAGGTAGCTAGCATGTAGACATTTTTCTCATAGATGATGGCCAAATCCATTCCACCA[G/A,T]
CAACAAAAATATGTAAAACATGACGATTTGCAGTAGTGACTAGGAATGAAAACGGATCGGAAACGGACGGAAACTAGCTTTATCATATTCGTTTTCATAT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 96.10% 3.20% 0.76% 0.00% A: 0.02%
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 87.90% 9.70% 2.38% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 84.50% 11.30% 4.17% 0.00% NA
Tropical Japonica  504 95.80% 4.20% 0.00% 0.00% NA
Japonica Intermediate  241 82.20% 16.20% 1.66% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 96.70% 2.20% 0.00% 0.00% A: 1.11%

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0136265772 C -> T LOC_Os01g62620.1 upstream_gene_variant ; 4043.0bp to feature; MODIFIER silent_mutation Average:47.842; most accessible tissue: Callus, score: 74.222 N N N N
vg0136265772 C -> T LOC_Os01g62620.2 upstream_gene_variant ; 4028.0bp to feature; MODIFIER silent_mutation Average:47.842; most accessible tissue: Callus, score: 74.222 N N N N
vg0136265772 C -> T LOC_Os01g62630.1 downstream_gene_variant ; 2291.0bp to feature; MODIFIER silent_mutation Average:47.842; most accessible tissue: Callus, score: 74.222 N N N N
vg0136265772 C -> T LOC_Os01g62620-LOC_Os01g62630 intergenic_region ; MODIFIER silent_mutation Average:47.842; most accessible tissue: Callus, score: 74.222 N N N N
vg0136265772 C -> A LOC_Os01g62620.1 upstream_gene_variant ; 4043.0bp to feature; MODIFIER silent_mutation Average:47.842; most accessible tissue: Callus, score: 74.222 N N N N
vg0136265772 C -> A LOC_Os01g62620.2 upstream_gene_variant ; 4028.0bp to feature; MODIFIER silent_mutation Average:47.842; most accessible tissue: Callus, score: 74.222 N N N N
vg0136265772 C -> A LOC_Os01g62630.1 downstream_gene_variant ; 2291.0bp to feature; MODIFIER silent_mutation Average:47.842; most accessible tissue: Callus, score: 74.222 N N N N
vg0136265772 C -> A LOC_Os01g62620-LOC_Os01g62630 intergenic_region ; MODIFIER silent_mutation Average:47.842; most accessible tissue: Callus, score: 74.222 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0136265772 4.24E-07 9.90E-09 Awn_length Jap_All YES Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0136265772 NA 3.60E-06 mr1496 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