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Detailed information for vg1014017091:

Variant ID: vg1014017091 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 14017091
Reference Allele: CAlternative Allele: T,A
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGTGGCAGTGGAGCCCAGTGGTGGGCAGATCCACCACCTCCGCTGTTACAGTGACGGCATCTTCTGAGGCGGTGGGAATGGGAGCTTCTGGCTAGGGATC[C/T,A]
TGGATTTTTTTTTTTGAATTTTCAAATTTTTTGGTGATTTTCTGGTGACATAATGCACCGCATGCAAAAGTTCATTATGGCACGTGATTCAGCCGCTCGG

Reverse complement sequence

CCGAGCGGCTGAATCACGTGCCATAATGAACTTTTGCATGCGGTGCATTATGTCACCAGAAAATCACCAAAAAATTTGAAAATTCAAAAAAAAAAATCCA[G/A,T]
GATCCCTAGCCAGAAGCTCCCATTCCCACCGCCTCAGAAGATGCCGTCACTGTAACAGCGGAGGTGGTGGATCTGCCCACCACTGGGCTCCACTGCCACC

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 93.20% 6.50% 0.11% 0.00% A: 0.15%
All Indica  2759 99.50% 0.50% 0.00% 0.00% NA
All Japonica  1512 81.00% 18.80% 0.26% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 98.70% 1.30% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.10% 0.90% 0.00% 0.00% NA
Temperate Japonica  767 95.80% 4.20% 0.00% 0.00% NA
Tropical Japonica  504 54.00% 45.20% 0.79% 0.00% NA
Japonica Intermediate  241 90.00% 10.00% 0.00% 0.00% NA
VI/Aromatic  96 94.80% 1.00% 0.00% 0.00% A: 4.17%
Intermediate  90 83.30% 12.20% 1.11% 0.00% A: 3.33%

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1014017091 C -> T LOC_Os10g26780.1 upstream_gene_variant ; 3258.0bp to feature; MODIFIER silent_mutation Average:53.549; most accessible tissue: Zhenshan97 young leaf, score: 75.751 N N N N
vg1014017091 C -> T LOC_Os10g26780-LOC_Os10g26800 intergenic_region ; MODIFIER silent_mutation Average:53.549; most accessible tissue: Zhenshan97 young leaf, score: 75.751 N N N N
vg1014017091 C -> A LOC_Os10g26780.1 upstream_gene_variant ; 3258.0bp to feature; MODIFIER silent_mutation Average:53.549; most accessible tissue: Zhenshan97 young leaf, score: 75.751 N N N N
vg1014017091 C -> A LOC_Os10g26780-LOC_Os10g26800 intergenic_region ; MODIFIER silent_mutation Average:53.549; most accessible tissue: Zhenshan97 young leaf, score: 75.751 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1014017091 NA 8.75E-06 mr1125 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
vg1014017091 NA 6.05E-06 mr1039_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
vg1014017091 2.60E-06 2.60E-06 mr1325_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
vg1014017091 NA 2.88E-09 mr1379_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
vg1014017091 NA 3.20E-07 mr1401_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
vg1014017091 NA 1.64E-07 mr1623_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
vg1014017091 NA 2.00E-08 mr1819_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
vg1014017091 NA 1.34E-10 mr1905_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