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Detailed information for vg1010359560:

Variant ID: vg1010359560 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 10359560
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CACAAAATATTTTGCTCCTCATAACCAGTCTATCAATTAGCACTGATTCGCTCTTTGTTGCTTGTTTTCCTACCTAGTAAAATAAAGTGCAGGAAAATAT[C/T]
CACTGTTGTGTCTTGGATGAAAGGTCTTCAGGTATTAATTAGCTCCCCCATCAGTGCTTGTTTTACCAAGGAAATCATTGATTATTTAGTCATCACTACC

Reverse complement sequence

GGTAGTGATGACTAAATAATCAATGATTTCCTTGGTAAAACAAGCACTGATGGGGGAGCTAATTAATACCTGAAGACCTTTCATCCAAGACACAACAGTG[G/A]
ATATTTTCCTGCACTTTATTTTACTAGGTAGGAAAACAAGCAACAAAGAGCGAATCAGTGCTAATTGATAGACTGGTTATGAGGAGCAAAATATTTTGTG

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 93.80% 6.20% 0.00% 0.00% NA
All Indica  2759 99.30% 0.70% 0.00% 0.00% NA
All Japonica  1512 84.50% 15.50% 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  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 98.70% 1.30% 0.00% 0.00% NA
Indica Intermediate  786 99.20% 0.80% 0.00% 0.00% NA
Temperate Japonica  767 93.40% 6.60% 0.00% 0.00% NA
Tropical Japonica  504 73.20% 26.80% 0.00% 0.00% NA
Japonica Intermediate  241 80.10% 19.90% 0.00% 0.00% NA
VI/Aromatic  96 74.00% 26.00% 0.00% 0.00% NA
Intermediate  90 83.30% 16.70% 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
vg1010359560 C -> T LOC_Os10g20560.1 upstream_gene_variant ; 543.0bp to feature; MODIFIER silent_mutation Average:38.103; most accessible tissue: Callus, score: 67.13 N N N N
vg1010359560 C -> T LOC_Os10g20540.1 downstream_gene_variant ; 4839.0bp to feature; MODIFIER silent_mutation Average:38.103; most accessible tissue: Callus, score: 67.13 N N N N
vg1010359560 C -> T LOC_Os10g20550.1 downstream_gene_variant ; 1028.0bp to feature; MODIFIER silent_mutation Average:38.103; most accessible tissue: Callus, score: 67.13 N N N N
vg1010359560 C -> T LOC_Os10g20550-LOC_Os10g20560 intergenic_region ; MODIFIER silent_mutation Average:38.103; most accessible tissue: Callus, score: 67.13 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1010359560 3.14E-06 NA mr1484 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
vg1010359560 9.11E-06 2.58E-07 mr1320_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
vg1010359560 1.48E-07 1.48E-07 mr1320_2 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