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Detailed information for vg0136199234:

Variant ID: vg0136199234 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 36199234
Reference Allele: TAlternative Allele: C,G
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATGAATCTAGACACACGTATATGTCTATATTCATTAGTATATATATAAATATGAGCAGTGCTAGAAAGTCTTATAATATAAAATAGAGGAAGTAATCTAG[T/C,G]
ACTCTGTACTAGATGCATTCTAGTATTAGATGTGAGCATATATATATATATATATATATATATATAGAGAGAGAGAGAGAGAATTTTTATGGTACTATAT

Reverse complement sequence

ATATAGTACCATAAAAATTCTCTCTCTCTCTCTCTATATATATATATATATATATATATATATGCTCACATCTAATACTAGAATGCATCTAGTACAGAGT[A/G,C]
CTAGATTACTTCCTCTATTTTATATTATAAGACTTTCTAGCACTGCTCATATTTATATATATACTAATGAATATAGACATATACGTGTGTCTAGATTCAT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 88.10% 10.70% 1.21% 0.00% G: 0.04%
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 63.80% 32.50% 3.70% 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 99.80% 0.20% 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 62.80% 31.30% 5.87% 0.00% NA
Tropical Japonica  504 57.70% 40.10% 2.18% 0.00% NA
Japonica Intermediate  241 79.30% 20.70% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 84.40% 12.20% 1.11% 0.00% G: 2.22%

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0136199234 T -> G LOC_Os01g62514.1 upstream_gene_variant ; 4623.0bp to feature; MODIFIER silent_mutation Average:50.323; most accessible tissue: Callus, score: 70.147 N N N N
vg0136199234 T -> G LOC_Os01g62514-LOC_Os01g62520 intergenic_region ; MODIFIER silent_mutation Average:50.323; most accessible tissue: Callus, score: 70.147 N N N N
vg0136199234 T -> C LOC_Os01g62514.1 upstream_gene_variant ; 4623.0bp to feature; MODIFIER silent_mutation Average:50.323; most accessible tissue: Callus, score: 70.147 N N N N
vg0136199234 T -> C LOC_Os01g62514-LOC_Os01g62520 intergenic_region ; MODIFIER silent_mutation Average:50.323; most accessible tissue: Callus, score: 70.147 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0136199234 2.23E-06 2.23E-06 mr1074_2 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
vg0136199234 NA 3.22E-06 mr1269_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
vg0136199234 NA 7.24E-06 mr1677_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
vg0136199234 NA 5.28E-10 mr1806_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