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Detailed information for vg0612193499:

Variant ID: vg0612193499 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 12193499
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTTCTATTTGGCTCAAATATAATAAACTACTTGTGGATACTCCGTATGTTGTAGCGGAAAATTTAAAAATACTTCAAAGAAAACTTGAAGAAAACAATTT[A/G]
TAAATCGTGTACACGTAATATCTATAAATGGACACTATTTGTTCTATAATAGTTGATGTGAAATTGTAATTCTACATGACACTTAGATGGTTATGTATCA

Reverse complement sequence

TGATACATAACCATCTAAGTGTCATGTAGAATTACAATTTCACATCAACTATTATAGAACAAATAGTGTCCATTTATAGATATTACGTGTACACGATTTA[T/C]
AAATTGTTTTCTTCAAGTTTTCTTTGAAGTATTTTTAAATTTTCCGCTACAACATACGGAGTATCCACAAGTAGTTTATTATATTTGAGCCAAATAGAAA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 67.90% 32.10% 0.04% 0.00% NA
All Indica  2759 95.60% 4.30% 0.07% 0.00% NA
All Japonica  1512 12.00% 88.00% 0.00% 0.00% NA
Aus  269 88.50% 11.50% 0.00% 0.00% NA
Indica I  595 93.80% 6.20% 0.00% 0.00% NA
Indica II  465 95.90% 3.90% 0.22% 0.00% NA
Indica III  913 99.60% 0.40% 0.00% 0.00% NA
Indica Intermediate  786 92.20% 7.60% 0.13% 0.00% NA
Temperate Japonica  767 3.00% 97.00% 0.00% 0.00% NA
Tropical Japonica  504 27.00% 73.00% 0.00% 0.00% NA
Japonica Intermediate  241 9.10% 90.90% 0.00% 0.00% NA
VI/Aromatic  96 92.70% 7.30% 0.00% 0.00% NA
Intermediate  90 67.80% 32.20% 0.00% 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
vg0612193499 A -> G LOC_Os06g21110.1 upstream_gene_variant ; 1244.0bp to feature; MODIFIER silent_mutation Average:38.217; most accessible tissue: Callus, score: 62.905 N N N N
vg0612193499 A -> G LOC_Os06g21120.2 upstream_gene_variant ; 3951.0bp to feature; MODIFIER silent_mutation Average:38.217; most accessible tissue: Callus, score: 62.905 N N N N
vg0612193499 A -> G LOC_Os06g21120.1 upstream_gene_variant ; 3951.0bp to feature; MODIFIER silent_mutation Average:38.217; most accessible tissue: Callus, score: 62.905 N N N N
vg0612193499 A -> G LOC_Os06g21099.1 downstream_gene_variant ; 2841.0bp to feature; MODIFIER silent_mutation Average:38.217; most accessible tissue: Callus, score: 62.905 N N N N
vg0612193499 A -> G LOC_Os06g21099-LOC_Os06g21110 intergenic_region ; MODIFIER silent_mutation Average:38.217; most accessible tissue: Callus, score: 62.905 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0612193499 2.36E-06 2.36E-06 mr1165 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
vg0612193499 NA 1.31E-06 mr1245 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
vg0612193499 NA 1.27E-17 mr1529 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
vg0612193499 NA 2.67E-08 mr1165_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
vg0612193499 2.49E-06 NA mr1211_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
vg0612193499 1.50E-10 2.27E-06 mr1211_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