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Detailed information for vg0630785612:

Variant ID: vg0630785612 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 30785612
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTCAACGTAGTTATTTTAGATTGGTTAAGTTACTAAGAACGTATATATAAAAGTTTTACCTACAAATTATTTTATATCAGTAATAAACCATTACGAGCTA[T/C]
AGGCAACCAACAGGGATCTAGATACATATTACCTCCGTTTACCTCCGTTCCTAAGTAAGTAGTACATTTCTAGCATAAGAAGCACAAATTAGTATAGTAG

Reverse complement sequence

CTACTATACTAATTTGTGCTTCTTATGCTAGAAATGTACTACTTACTTAGGAACGGAGGTAAACGGAGGTAATATGTATCTAGATCCCTGTTGGTTGCCT[A/G]
TAGCTCGTAATGGTTTATTACTGATATAAAATAATTTGTAGGTAAAACTTTTATATATACGTTCTTAGTAACTTAACCAATCTAAAATAACTACGTTGAG

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 93.60% 6.40% 0.02% 0.00% NA
All Indica  2759 99.70% 0.30% 0.04% 0.00% NA
All Japonica  1512 81.20% 18.80% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 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 99.30% 0.70% 0.00% 0.00% NA
Indica Intermediate  786 99.70% 0.10% 0.13% 0.00% NA
Temperate Japonica  767 94.90% 5.10% 0.00% 0.00% NA
Tropical Japonica  504 66.50% 33.50% 0.00% 0.00% NA
Japonica Intermediate  241 68.00% 32.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 92.20% 7.80% 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
vg0630785612 T -> C LOC_Os06g50890.1 downstream_gene_variant ; 1973.0bp to feature; MODIFIER silent_mutation Average:73.479; most accessible tissue: Minghui63 panicle, score: 85.069 N N N N
vg0630785612 T -> C LOC_Os06g50890-LOC_Os06g50910 intergenic_region ; MODIFIER silent_mutation Average:73.479; most accessible tissue: Minghui63 panicle, score: 85.069 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0630785612 5.30E-09 NA Grain_weight All Not 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
vg0630785612 1.30E-08 NA mr1188 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
vg0630785612 1.20E-06 1.22E-07 mr1188 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
vg0630785612 NA 1.18E-06 mr1700 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
vg0630785612 NA 1.96E-07 mr1188_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
vg0630785612 NA 5.47E-09 mr1449_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