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Detailed information for vg1001652766:

Variant ID: vg1001652766 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 1652766
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTTCTAAGATTATTGGATTTTTGGTCTAAAGGAAAAAGGATTTAATTAAACCCTTTTGAAAAAGAAAAGAAAGAGGGAGGGGAAACAGACTTCCCTCGGG[T/C]
GGCTAGGGCGCGGCCCGAGAGAAAGGGGCGGCTCGGCCGAGCTTAATGGGCCGGCCGGCCCGAGAAGACGGCCCGAAGGCACGCGCGGGAGGGGAGGAGA

Reverse complement sequence

TCTCCTCCCCTCCCGCGCGTGCCTTCGGGCCGTCTTCTCGGGCCGGCCGGCCCATTAAGCTCGGCCGAGCCGCCCCTTTCTCTCGGGCCGCGCCCTAGCC[A/G]
CCCGAGGGAAGTCTGTTTCCCCTCCCTCTTTCTTTTCTTTTTCAAAAGGGTTTAATTAAATCCTTTTTCCTTTAGACCAAAAATCCAATAATCTTAGAAA

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 43.50% 42.70% 5.18% 8.59% NA
All Indica  2759 14.10% 64.60% 7.14% 14.17% NA
All Japonica  1512 94.30% 5.20% 0.00% 0.46% NA
Aus  269 36.80% 46.80% 15.61% 0.74% NA
Indica I  595 13.90% 54.80% 5.04% 26.22% NA
Indica II  465 9.20% 66.50% 9.25% 15.05% NA
Indica III  913 14.80% 68.30% 7.78% 9.09% NA
Indica Intermediate  786 16.40% 66.40% 6.74% 10.43% NA
Temperate Japonica  767 98.60% 1.40% 0.00% 0.00% NA
Tropical Japonica  504 86.10% 12.70% 0.00% 1.19% NA
Japonica Intermediate  241 97.90% 1.70% 0.00% 0.41% NA
VI/Aromatic  96 92.70% 6.20% 1.04% 0.00% NA
Intermediate  90 60.00% 27.80% 5.56% 6.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1001652766 T -> C LOC_Os10g03690.1 downstream_gene_variant ; 3838.0bp to feature; MODIFIER silent_mutation Average:34.274; most accessible tissue: Minghui63 panicle, score: 82.797 N N N N
vg1001652766 T -> C LOC_Os10g03669-LOC_Os10g03690 intergenic_region ; MODIFIER silent_mutation Average:34.274; most accessible tissue: Minghui63 panicle, score: 82.797 N N N N
vg1001652766 T -> DEL N N silent_mutation Average:34.274; most accessible tissue: Minghui63 panicle, score: 82.797 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1001652766 NA 2.28E-15 mr1323 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
vg1001652766 2.63E-06 NA mr1486 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
vg1001652766 2.26E-07 6.73E-08 mr1486 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
vg1001652766 NA 2.77E-06 mr1622 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
vg1001652766 NA 2.37E-06 mr1486_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