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Detailed information for vg1117161706:

Variant ID: vg1117161706 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 17161706
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, T: 0.01, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:


TCGCCGCATCCACCCTCCTCGCCAGCGCCGGCGCCACCGCAACTGTCACGTCCTGATAAATTCATCCTGAATTAAAAATCATTCTCTAAAAGGAATAATA[G/T]
AATTAATTAAAATTCGAAAAGAAATTGGCAAACACTAAAATACGTACTAGAAAAATTCGAATGTTGTCCGGAGATTTTTTGTTAAATTCTCCATGGTCTA

Reverse complement sequence

TAGACCATGGAGAATTTAACAAAAAATCTCCGGACAACATTCGAATTTTTCTAGTACGTATTTTAGTGTTTGCCAATTTCTTTTCGAATTTTAATTAATT[C/A]
TATTATTCCTTTTAGAGAATGATTTTTAATTCAGGATGAATTTATCAGGACGTGACAGTTGCGGTGGCGCCGGCGCTGGCGAGGAGGGTGGATGCGGCGA

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 66.00% 11.00% 6.47% 16.53% NA
All Indica  2759 70.20% 18.40% 7.21% 4.17% NA
All Japonica  1512 61.40% 0.30% 2.18% 36.11% NA
Aus  269 65.80% 0.00% 21.93% 12.27% NA
Indica I  595 88.70% 5.50% 1.85% 3.87% NA
Indica II  465 68.80% 14.20% 11.40% 5.59% NA
Indica III  913 58.70% 30.40% 7.34% 3.50% NA
Indica Intermediate  786 70.40% 16.70% 8.65% 4.33% NA
Temperate Japonica  767 87.90% 0.10% 0.91% 11.08% NA
Tropical Japonica  504 35.30% 0.60% 4.37% 59.72% NA
Japonica Intermediate  241 32.00% 0.00% 1.66% 66.39% NA
VI/Aromatic  96 11.50% 2.10% 8.33% 78.12% NA
Intermediate  90 71.10% 7.80% 7.78% 13.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1117161706 G -> T LOC_Os11g29570.1 upstream_gene_variant ; 3025.0bp to feature; MODIFIER silent_mutation Average:28.968; most accessible tissue: Callus, score: 49.336 N N N N
vg1117161706 G -> T LOC_Os11g29580.1 downstream_gene_variant ; 1038.0bp to feature; MODIFIER silent_mutation Average:28.968; most accessible tissue: Callus, score: 49.336 N N N N
vg1117161706 G -> T LOC_Os11g29570-LOC_Os11g29580 intergenic_region ; MODIFIER silent_mutation Average:28.968; most accessible tissue: Callus, score: 49.336 N N N N
vg1117161706 G -> DEL N N silent_mutation Average:28.968; most accessible tissue: Callus, score: 49.336 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1117161706 NA 4.73E-06 mr1030 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
vg1117161706 NA 3.41E-06 mr1046 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
vg1117161706 NA 2.22E-06 mr1048 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
vg1117161706 NA 5.14E-07 mr1053 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
vg1117161706 NA 6.74E-06 mr1054 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
vg1117161706 NA 2.39E-06 mr1115 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
vg1117161706 NA 3.50E-06 mr1170 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
vg1117161706 NA 6.08E-07 mr1230 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
vg1117161706 7.28E-06 7.28E-06 mr1230 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
vg1117161706 NA 5.83E-06 mr1287 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
vg1117161706 NA 4.60E-06 mr1353 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
vg1117161706 NA 4.34E-06 mr1372 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
vg1117161706 NA 8.23E-06 mr1377 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
vg1117161706 NA 2.94E-06 mr1378 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
vg1117161706 NA 5.81E-06 mr1380 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
vg1117161706 8.22E-07 8.23E-07 mr1391 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
vg1117161706 NA 6.84E-07 mr1428 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
vg1117161706 NA 1.31E-07 mr1432 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
vg1117161706 NA 4.63E-06 mr1512 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
vg1117161706 NA 6.57E-06 mr1550 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
vg1117161706 NA 2.96E-06 mr1614 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
vg1117161706 NA 8.74E-06 mr1635 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
vg1117161706 NA 8.83E-06 mr1724 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
vg1117161706 NA 2.15E-06 mr1749 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
vg1117161706 NA 6.23E-07 mr1807 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
vg1117161706 NA 7.02E-06 mr1821 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
vg1117161706 2.69E-06 2.71E-06 mr1869 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
vg1117161706 6.30E-07 6.30E-07 mr1869 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
vg1117161706 NA 2.61E-06 mr1941 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