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Detailed information for vg0602179233:

Variant ID: vg0602179233 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 2179233
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTGTAAAGAAAATTTTCGCATAAAATATATTATTTTTAGTAGTTTGAAAAACGTGCTAAAAATCAGTATCTTAATTAGAAAAGAACGAGCCCAGGATACA[A/T]
CCAACTTTGCTTTACTGATAATTTACTGAAAACTCCTCTTTTTTTGTGTGTTCTTAATTAATAACAACCAACGGGGTTCACAAAACCGATCAGTTTTCGT

Reverse complement sequence

ACGAAAACTGATCGGTTTTGTGAACCCCGTTGGTTGTTATTAATTAAGAACACACAAAAAAAGAGGAGTTTTCAGTAAATTATCAGTAAAGCAAAGTTGG[T/A]
TGTATCCTGGGCTCGTTCTTTTCTAATTAAGATACTGATTTTTAGCACGTTTTTCAAACTACTAAAAATAATATATTTTATGCGAAAATTTTCTTTACAA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 95.90% 3.60% 0.51% 0.00% NA
All Indica  2759 97.80% 2.00% 0.22% 0.00% NA
All Japonica  1512 91.90% 7.00% 1.06% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.80% 0.00% 0.17% 0.00% NA
Indica II  465 94.40% 4.90% 0.65% 0.00% NA
Indica III  913 99.70% 0.30% 0.00% 0.00% NA
Indica Intermediate  786 95.90% 3.80% 0.25% 0.00% NA
Temperate Japonica  767 99.60% 0.10% 0.26% 0.00% NA
Tropical Japonica  504 77.80% 20.00% 2.18% 0.00% NA
Japonica Intermediate  241 97.10% 1.70% 1.24% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 90.00% 7.80% 2.22% 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
vg0602179233 A -> T LOC_Os06g04940.1 upstream_gene_variant ; 2307.0bp to feature; MODIFIER silent_mutation Average:35.792; most accessible tissue: Minghui63 panicle, score: 75.788 N N N N
vg0602179233 A -> T LOC_Os06g04940.2 upstream_gene_variant ; 2307.0bp to feature; MODIFIER silent_mutation Average:35.792; most accessible tissue: Minghui63 panicle, score: 75.788 N N N N
vg0602179233 A -> T LOC_Os06g04950.1 downstream_gene_variant ; 965.0bp to feature; MODIFIER silent_mutation Average:35.792; most accessible tissue: Minghui63 panicle, score: 75.788 N N N N
vg0602179233 A -> T LOC_Os06g04940-LOC_Os06g04950 intergenic_region ; MODIFIER silent_mutation Average:35.792; most accessible tissue: Minghui63 panicle, score: 75.788 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0602179233 6.09E-06 NA mr1016 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
vg0602179233 4.83E-06 NA mr1017 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
vg0602179233 2.76E-06 NA mr1055 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