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Detailed information for vg1007445967:

Variant ID: vg1007445967 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 7445967
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.77, C: 0.23, others allele: 0.00, population size: 100. )

Flanking Sequence (100 bp) in Reference Genome:


ATAGAAACCAATCCAAATGAGATTTGAGAGTTTTCTATTTGCCGTATAAATTTCATCAGAGGCCAGTGACGTTTCACTGGTATAGAACACCCTATAGGTG[C/T]
TGGTTGGGAATCTCACATAGGTGCCAGTTTCCCAACTGGCAACCGATGCCACTAAGGCAAAACTAATGAAATCATAGGTGTCGGTTTAGAAATTAGCACC

Reverse complement sequence

GGTGCTAATTTCTAAACCGACACCTATGATTTCATTAGTTTTGCCTTAGTGGCATCGGTTGCCAGTTGGGAAACTGGCACCTATGTGAGATTCCCAACCA[G/A]
CACCTATAGGGTGTTCTATACCAGTGAAACGTCACTGGCCTCTGATGAAATTTATACGGCAAATAGAAAACTCTCAAATCTCATTTGGATTGGTTTCTAT

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 65.40% 34.00% 0.40% 0.17% NA
All Indica  2759 64.00% 35.30% 0.43% 0.25% NA
All Japonica  1512 62.50% 37.10% 0.40% 0.00% NA
Aus  269 99.60% 0.00% 0.37% 0.00% NA
Indica I  595 13.40% 86.10% 0.00% 0.50% NA
Indica II  465 83.00% 15.50% 0.86% 0.65% NA
Indica III  913 83.00% 16.60% 0.33% 0.00% NA
Indica Intermediate  786 69.00% 30.30% 0.64% 0.13% NA
Temperate Japonica  767 58.40% 41.30% 0.26% 0.00% NA
Tropical Japonica  504 58.10% 41.10% 0.79% 0.00% NA
Japonica Intermediate  241 84.60% 15.40% 0.00% 0.00% NA
VI/Aromatic  96 52.10% 47.90% 0.00% 0.00% NA
Intermediate  90 67.80% 31.10% 0.00% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1007445967 C -> T LOC_Os10g13700.2 upstream_gene_variant ; 1859.0bp to feature; MODIFIER silent_mutation Average:69.512; most accessible tissue: Callus, score: 87.757 N N N N
vg1007445967 C -> T LOC_Os10g13694.1 downstream_gene_variant ; 3958.0bp to feature; MODIFIER silent_mutation Average:69.512; most accessible tissue: Callus, score: 87.757 N N N N
vg1007445967 C -> T LOC_Os10g13694.3 downstream_gene_variant ; 4132.0bp to feature; MODIFIER silent_mutation Average:69.512; most accessible tissue: Callus, score: 87.757 N N N N
vg1007445967 C -> T LOC_Os10g13694.2 downstream_gene_variant ; 3952.0bp to feature; MODIFIER silent_mutation Average:69.512; most accessible tissue: Callus, score: 87.757 N N N N
vg1007445967 C -> T LOC_Os10g13700-LOC_Os10g13710 intergenic_region ; MODIFIER silent_mutation Average:69.512; most accessible tissue: Callus, score: 87.757 N N N N
vg1007445967 C -> DEL N N silent_mutation Average:69.512; most accessible tissue: Callus, score: 87.757 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1007445967 1.33E-06 NA mr1026 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
vg1007445967 1.71E-10 5.58E-24 mr1026 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
vg1007445967 NA 4.65E-08 mr1113 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
vg1007445967 NA 3.94E-08 mr1114 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
vg1007445967 NA 6.22E-07 mr1116 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
vg1007445967 1.26E-11 3.57E-24 mr1118 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
vg1007445967 NA 4.68E-08 mr1120 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
vg1007445967 1.22E-06 NA mr1161 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
vg1007445967 1.18E-10 5.82E-23 mr1161 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
vg1007445967 NA 1.92E-06 mr1242 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
vg1007445967 NA 8.46E-06 mr1261 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
vg1007445967 7.75E-06 NA mr1495 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
vg1007445967 9.46E-11 3.26E-29 mr1495 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
vg1007445967 NA 2.54E-11 mr1496 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
vg1007445967 9.23E-07 3.56E-11 mr1794 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
vg1007445967 6.51E-07 1.26E-13 mr1794 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
vg1007445967 NA 9.74E-07 mr1936 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
vg1007445967 1.39E-06 9.07E-08 mr1113_2 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
vg1007445967 1.01E-06 6.88E-08 mr1114_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
vg1007445967 NA 7.17E-06 mr1117_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
vg1007445967 4.31E-09 8.45E-30 mr1118_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
vg1007445967 NA 6.60E-06 mr1119_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
vg1007445967 5.50E-07 4.07E-10 mr1120_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
vg1007445967 NA 1.37E-07 mr1123_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
vg1007445967 2.50E-06 NA mr1161_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
vg1007445967 5.89E-08 5.56E-22 mr1161_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
vg1007445967 NA 6.16E-06 mr1233_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
vg1007445967 3.39E-06 2.09E-07 mr1247_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
vg1007445967 1.48E-08 2.46E-32 mr1495_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
vg1007445967 NA 6.39E-10 mr1496_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
vg1007445967 NA 1.59E-07 mr1531_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
vg1007445967 NA 1.04E-10 mr1709_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
vg1007445967 3.89E-06 4.85E-17 mr1794_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
vg1007445967 NA 8.57E-11 mr1936_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
vg1007445967 NA 6.89E-07 mr1961_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