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Detailed information for vg1006731965:

Variant ID: vg1006731965 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 6731965
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, T: 0.01, others allele: 0.00, population size: 108. )

Flanking Sequence (100 bp) in Reference Genome:


GCCGAGATCAGCTGCCGCTCGCTGTCGCCGCCACCGGTCTGACCACCCGTATGCCGCCGGTCTGACCACCGCTTGCCGCCGGTCTGACCGCCGGTAGATC[G/T]
CCAGTTAGACCGCCGAAACTCGGTAAACACAAATCGAAGAACTCTTAAAGTGGATGACGACTATATTAATTCTCTCTGTGTTTACAAAGTGCACCAACAG

Reverse complement sequence

CTGTTGGTGCACTTTGTAAACACAGAGAGAATTAATATAGTCGTCATCCACTTTAAGAGTTCTTCGATTTGTGTTTACCGAGTTTCGGCGGTCTAACTGG[C/A]
GATCTACCGGCGGTCAGACCGGCGGCAAGCGGTGGTCAGACCGGCGGCATACGGGTGGTCAGACCGGTGGCGGCGACAGCGAGCGGCAGCTGATCTCGGC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 33.50% 21.50% 1.82% 43.21% NA
All Indica  2759 5.70% 35.90% 2.39% 56.00% NA
All Japonica  1512 67.70% 0.90% 1.12% 30.36% NA
Aus  269 98.10% 0.00% 0.37% 1.49% NA
Indica I  595 1.80% 87.60% 0.34% 10.25% NA
Indica II  465 1.90% 17.40% 1.72% 78.92% NA
Indica III  913 7.60% 15.40% 3.83% 73.17% NA
Indica Intermediate  786 8.80% 31.40% 2.67% 57.12% NA
Temperate Japonica  767 88.70% 0.80% 0.65% 9.91% NA
Tropical Japonica  504 39.10% 0.80% 2.38% 57.74% NA
Japonica Intermediate  241 60.60% 1.20% 0.00% 38.17% NA
VI/Aromatic  96 97.90% 0.00% 0.00% 2.08% NA
Intermediate  90 48.90% 13.30% 2.22% 35.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1006731965 G -> T LOC_Os10g12110.1 upstream_gene_variant ; 3812.0bp to feature; MODIFIER silent_mutation Average:34.72; most accessible tissue: Zhenshan97 flag leaf, score: 78.0 N N N N
vg1006731965 G -> T LOC_Os10g12120.1 downstream_gene_variant ; 268.0bp to feature; MODIFIER silent_mutation Average:34.72; most accessible tissue: Zhenshan97 flag leaf, score: 78.0 N N N N
vg1006731965 G -> T LOC_Os10g12130.1 downstream_gene_variant ; 697.0bp to feature; MODIFIER silent_mutation Average:34.72; most accessible tissue: Zhenshan97 flag leaf, score: 78.0 N N N N
vg1006731965 G -> T LOC_Os10g12120-LOC_Os10g12130 intergenic_region ; MODIFIER silent_mutation Average:34.72; most accessible tissue: Zhenshan97 flag leaf, score: 78.0 N N N N
vg1006731965 G -> DEL N N silent_mutation Average:34.72; most accessible tissue: Zhenshan97 flag leaf, score: 78.0 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1006731965 1.64E-07 1.24E-39 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
vg1006731965 1.12E-08 8.56E-23 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
vg1006731965 NA 3.13E-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
vg1006731965 8.19E-06 5.88E-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
vg1006731965 NA 1.28E-06 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
vg1006731965 6.10E-07 4.01E-18 mr1118 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
vg1006731965 6.88E-11 3.79E-23 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
vg1006731965 NA 3.93E-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
vg1006731965 4.59E-07 9.39E-37 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
vg1006731965 2.04E-08 5.18E-21 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
vg1006731965 9.22E-09 2.09E-25 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
vg1006731965 2.20E-11 2.00E-28 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
vg1006731965 NA 1.32E-09 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
vg1006731965 NA 4.55E-06 mr1789 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
vg1006731965 NA 4.15E-11 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
vg1006731965 NA 5.09E-06 mr1113_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
vg1006731965 NA 5.38E-06 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
vg1006731965 2.92E-06 4.25E-23 mr1118_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
vg1006731965 1.14E-12 2.36E-32 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
vg1006731965 NA 3.76E-09 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
vg1006731965 NA 3.00E-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
vg1006731965 1.04E-09 5.77E-43 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
vg1006731965 2.84E-12 2.93E-26 mr1161_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
vg1006731965 NA 1.70E-06 mr1242_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
vg1006731965 NA 8.14E-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
vg1006731965 8.11E-07 5.24E-32 mr1495_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
vg1006731965 1.50E-11 6.99E-33 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
vg1006731965 NA 1.60E-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
vg1006731965 NA 1.33E-08 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
vg1006731965 NA 8.15E-06 mr1580_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
vg1006731965 NA 4.36E-15 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
vg1006731965 NA 5.92E-06 mr1825_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
vg1006731965 NA 9.07E-07 mr1904_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
vg1006731965 NA 3.99E-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
vg1006731965 NA 3.03E-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