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Detailed information for vg0610635812:

Variant ID: vg0610635812 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 10635812
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCGAACAAACTTCGCGTTCCACTTTCTTGTATTCTCGCTTGGAGGAGTACGTCATGGAGCCGCCGAAGATGTGTGAAACATGGAGGTCGGAGTCTGGGTA[C/T]
GCGAAGTCCGATTCGTGAGGAGGTGACTCCTCGTTTTTCTCGACAACGCGTACTCGCTTGCCTTTTTCAAACGCCATGTGCTTCTCGGGCGACTTTTTGA

Reverse complement sequence

TCAAAAAGTCGCCCGAGAAGCACATGGCGTTTGAAAAAGGCAAGCGAGTACGCGTTGTCGAGAAAAACGAGGAGTCACCTCCTCACGAATCGGACTTCGC[G/A]
TACCCAGACTCCGACCTCCATGTTTCACACATCTTCGGCGGCTCCATGACGTACTCCTCCAAGCGAGAATACAAGAAAGTGGAACGCGAAGTTTGTTCGA

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 46.00% 0.10% 16.02% 37.88% NA
All Indica  2759 20.80% 0.20% 24.90% 54.11% NA
All Japonica  1512 82.50% 0.00% 0.93% 16.60% NA
Aus  269 83.60% 0.00% 12.64% 3.72% NA
Indica I  595 18.30% 0.00% 4.87% 76.81% NA
Indica II  465 5.80% 0.40% 14.19% 79.57% NA
Indica III  913 26.00% 0.40% 42.83% 30.78% NA
Indica Intermediate  786 25.40% 0.00% 25.57% 48.98% NA
Temperate Japonica  767 87.60% 0.00% 0.13% 12.26% NA
Tropical Japonica  504 71.00% 0.00% 1.59% 27.38% NA
Japonica Intermediate  241 90.00% 0.00% 2.07% 7.88% NA
VI/Aromatic  96 90.60% 0.00% 4.17% 5.21% NA
Intermediate  90 45.60% 0.00% 20.00% 34.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0610635812 C -> T LOC_Os06g18750.1 downstream_gene_variant ; 4590.0bp to feature; MODIFIER silent_mutation Average:11.895; most accessible tissue: Callus, score: 34.578 N N N N
vg0610635812 C -> T LOC_Os06g18750-LOC_Os06g18770 intergenic_region ; MODIFIER silent_mutation Average:11.895; most accessible tissue: Callus, score: 34.578 N N N N
vg0610635812 C -> DEL N N silent_mutation Average:11.895; most accessible tissue: Callus, score: 34.578 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0610635812 NA 5.90E-07 mr1002 Ind_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
vg0610635812 6.29E-06 NA mr1065 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
vg0610635812 2.56E-08 NA mr1087 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
vg0610635812 3.93E-09 3.73E-09 mr1087 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
vg0610635812 4.83E-07 NA mr1091 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
vg0610635812 4.10E-06 NA mr1094 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
vg0610635812 NA 3.26E-08 mr1094 Ind_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
vg0610635812 2.51E-06 NA mr1108 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
vg0610635812 1.13E-06 NA mr1234 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
vg0610635812 NA 1.31E-09 mr1299 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
vg0610635812 NA 3.14E-06 mr1345 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
vg0610635812 NA 9.81E-09 mr1465 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
vg0610635812 NA 1.72E-07 mr1727 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
vg0610635812 NA 3.65E-07 mr1756 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
vg0610635812 NA 1.24E-06 mr1761 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
vg0610635812 NA 2.01E-29 mr1877 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
vg0610635812 NA 1.95E-08 mr1877 Ind_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
vg0610635812 NA 1.70E-08 mr1094_2 Ind_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
vg0610635812 NA 1.35E-06 mr1096_2 Ind_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