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Detailed information for vg0701643483:

Variant ID: vg0701643483 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 1643483
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.04, others allele: 0.00, population size: 209. )

Flanking Sequence (100 bp) in Reference Genome:


CTAGGATTTAGGCCAAGACATGGTAGAAGCAGTCGGTAATTTACATCTCTTGGCTGCCATGAAGTCCAACAACATCGACATTAGGTGTTCGCCATTTTCT[C/T]
GGAAAAGTTGCATCACTCCCATCTTGAAAATTGAAGATGTCACTTGCAAACTATGGTACCAGCATAGACTATATTATTGCAGGTGAAGAAGAAATAGACC

Reverse complement sequence

GGTCTATTTCTTCTTCACCTGCAATAATATAGTCTATGCTGGTACCATAGTTTGCAAGTGACATCTTCAATTTTCAAGATGGGAGTGATGCAACTTTTCC[G/A]
AGAAAATGGCGAACACCTAATGTCGATGTTGTTGGACTTCATGGCAGCCAAGAGATGTAAATTACCGACTGCTTCTACCATGTCTTGGCCTAAATCCTAG

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 37.70% 4.10% 0.49% 57.70% NA
All Indica  2759 54.90% 0.80% 0.33% 43.89% NA
All Japonica  1512 10.70% 0.00% 0.79% 88.49% NA
Aus  269 5.20% 62.80% 0.37% 31.60% NA
Indica I  595 62.20% 0.20% 0.50% 37.14% NA
Indica II  465 45.20% 0.20% 0.43% 54.19% NA
Indica III  913 56.60% 0.40% 0.22% 42.72% NA
Indica Intermediate  786 53.30% 2.20% 0.25% 44.27% NA
Temperate Japonica  767 16.90% 0.00% 1.43% 81.62% NA
Tropical Japonica  504 4.20% 0.00% 0.00% 95.83% NA
Japonica Intermediate  241 4.60% 0.00% 0.41% 95.02% NA
VI/Aromatic  96 44.80% 1.00% 1.04% 53.12% NA
Intermediate  90 51.10% 2.20% 0.00% 46.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0701643483 C -> DEL N N silent_mutation Average:10.625; most accessible tissue: Callus, score: 57.376 N N N N
vg0701643483 C -> T LOC_Os07g03920.1 upstream_gene_variant ; 231.0bp to feature; MODIFIER silent_mutation Average:10.625; most accessible tissue: Callus, score: 57.376 N N N N
vg0701643483 C -> T LOC_Os07g03910.1 downstream_gene_variant ; 4873.0bp to feature; MODIFIER silent_mutation Average:10.625; most accessible tissue: Callus, score: 57.376 N N N N
vg0701643483 C -> T LOC_Os07g03930.1 downstream_gene_variant ; 3530.0bp to feature; MODIFIER silent_mutation Average:10.625; most accessible tissue: Callus, score: 57.376 N N N N
vg0701643483 C -> T LOC_Os07g03920-LOC_Os07g03930 intergenic_region ; MODIFIER silent_mutation Average:10.625; most accessible tissue: Callus, score: 57.376 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0701643483 NA 2.57E-06 mr1006 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
vg0701643483 NA 8.22E-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
vg0701643483 NA 7.10E-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
vg0701643483 NA 3.66E-06 mr1052 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
vg0701643483 NA 3.52E-07 mr1058 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
vg0701643483 NA 8.29E-08 mr1060 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
vg0701643483 NA 7.53E-08 mr1073 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
vg0701643483 NA 1.95E-06 mr1207 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
vg0701643483 NA 2.64E-06 mr1229 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
vg0701643483 NA 1.33E-06 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
vg0701643483 NA 2.09E-13 mr1231 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
vg0701643483 NA 1.53E-06 mr1283 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
vg0701643483 NA 9.69E-07 mr1286 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
vg0701643483 NA 1.39E-07 mr1345 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
vg0701643483 NA 5.75E-06 mr1358 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
vg0701643483 NA 2.18E-06 mr1365 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
vg0701643483 NA 1.71E-07 mr1417 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
vg0701643483 NA 9.85E-06 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
vg0701643483 NA 4.61E-06 mr1474 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
vg0701643483 NA 4.61E-06 mr1475 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
vg0701643483 NA 1.70E-06 mr1485 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
vg0701643483 NA 4.00E-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
vg0701643483 NA 3.33E-44 mr1549 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
vg0701643483 NA 8.90E-55 mr1550 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
vg0701643483 NA 1.17E-06 mr1556 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
vg0701643483 NA 2.78E-07 mr1621 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
vg0701643483 NA 3.99E-07 mr1665 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
vg0701643483 NA 4.16E-45 mr1757 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
vg0701643483 NA 1.49E-08 mr1762 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
vg0701643483 NA 4.20E-10 mr1774 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
vg0701643483 NA 7.84E-06 mr1928 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
vg0701643483 NA 2.62E-10 mr1931 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
vg0701643483 NA 1.29E-07 mr1942 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
vg0701643483 NA 8.17E-08 mr1510_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
vg0701643483 NA 1.76E-43 mr1549_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
vg0701643483 NA 6.20E-59 mr1550_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
vg0701643483 NA 1.71E-34 mr1757_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
vg0701643483 NA 3.02E-12 mr1803_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