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Detailed information for vg0907515920:

Variant ID: vg0907515920 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 7515920
Reference Allele: CAlternative Allele: T,G
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.87, T: 0.13, others allele: 0.00, population size: 85. )

Flanking Sequence (100 bp) in Reference Genome:


CAATGAATTTCTCGAATCCAACTTGCCACGCATCATCTGACTGAGACAATAGCATCCAACTATGATCATCATCACATGCCATATTCCAAGTGAGAAAATC[C/T,G]
GTTACCAAATTTGCCTAAGGGATAGTATGCAATGAAATAAACCAAATTTTAATTACATAGATATATAGAAAAAAAGAATCAACAGTTTTCATTGCACTCG

Reverse complement sequence

CGAGTGCAATGAAAACTGTTGATTCTTTTTTTCTATATATCTATGTAATTAAAATTTGGTTTATTTCATTGCATACTATCCCTTAGGCAAATTTGGTAAC[G/A,C]
GATTTTCTCACTTGGAATATGGCATGTGATGATGATCATAGTTGGATGCTATTGTCTCAGTCAGATGATGCGTGGCAAGTTGGATTCGAGAAATTCATTG

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 53.90% 44.70% 1.27% 0.13% NA
All Indica  2759 41.20% 56.80% 1.81% 0.18% NA
All Japonica  1512 79.40% 20.40% 0.13% 0.00% NA
Aus  269 17.50% 79.20% 2.97% 0.37% NA
Indica I  595 11.60% 84.70% 3.70% 0.00% NA
Indica II  465 75.90% 22.40% 1.51% 0.22% NA
Indica III  913 43.40% 55.00% 1.31% 0.33% NA
Indica Intermediate  786 40.70% 58.00% 1.15% 0.13% NA
Temperate Japonica  767 91.90% 8.00% 0.13% 0.00% NA
Tropical Japonica  504 76.00% 24.00% 0.00% 0.00% NA
Japonica Intermediate  241 46.90% 52.70% 0.41% 0.00% NA
VI/Aromatic  96 95.80% 4.20% 0.00% 0.00% NA
Intermediate  90 75.60% 24.40% 0.00% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0907515920 C -> G LOC_Os09g13020.1 upstream_gene_variant ; 3210.0bp to feature; MODIFIER N Average:46.777; most accessible tissue: Minghui63 young leaf, score: 66.656 N N N N
vg0907515920 C -> G LOC_Os09g13030.1 upstream_gene_variant ; 166.0bp to feature; MODIFIER N Average:46.777; most accessible tissue: Minghui63 young leaf, score: 66.656 N N N N
vg0907515920 C -> G LOC_Os09g13040.1 upstream_gene_variant ; 3120.0bp to feature; MODIFIER N Average:46.777; most accessible tissue: Minghui63 young leaf, score: 66.656 N N N N
vg0907515920 C -> G LOC_Os09g13010.1 downstream_gene_variant ; 4085.0bp to feature; MODIFIER N Average:46.777; most accessible tissue: Minghui63 young leaf, score: 66.656 N N N N
vg0907515920 C -> G LOC_Os09g13030-LOC_Os09g13040 intergenic_region ; MODIFIER N Average:46.777; most accessible tissue: Minghui63 young leaf, score: 66.656 N N N N
vg0907515920 C -> DEL N N silent_mutation Average:46.777; most accessible tissue: Minghui63 young leaf, score: 66.656 N N N N
vg0907515920 C -> T LOC_Os09g13020.1 upstream_gene_variant ; 3210.0bp to feature; MODIFIER silent_mutation Average:46.777; most accessible tissue: Minghui63 young leaf, score: 66.656 N N N N
vg0907515920 C -> T LOC_Os09g13030.1 upstream_gene_variant ; 166.0bp to feature; MODIFIER silent_mutation Average:46.777; most accessible tissue: Minghui63 young leaf, score: 66.656 N N N N
vg0907515920 C -> T LOC_Os09g13040.1 upstream_gene_variant ; 3120.0bp to feature; MODIFIER silent_mutation Average:46.777; most accessible tissue: Minghui63 young leaf, score: 66.656 N N N N
vg0907515920 C -> T LOC_Os09g13010.1 downstream_gene_variant ; 4085.0bp to feature; MODIFIER silent_mutation Average:46.777; most accessible tissue: Minghui63 young leaf, score: 66.656 N N N N
vg0907515920 C -> T LOC_Os09g13030-LOC_Os09g13040 intergenic_region ; MODIFIER silent_mutation Average:46.777; most accessible tissue: Minghui63 young leaf, score: 66.656 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0907515920 NA 1.49E-06 mr1498 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
vg0907515920 NA 1.03E-06 mr1598 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
vg0907515920 NA 9.73E-10 mr1607 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
vg0907515920 NA 1.21E-06 mr1159_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
vg0907515920 NA 4.87E-07 mr1296_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
vg0907515920 NA 3.78E-06 mr1296_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
vg0907515920 NA 5.88E-08 mr1299_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
vg0907515920 NA 5.70E-07 mr1321_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
vg0907515920 NA 2.84E-06 mr1321_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
vg0907515920 NA 4.42E-07 mr1322_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
vg0907515920 NA 5.03E-09 mr1332_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
vg0907515920 NA 8.11E-07 mr1332_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
vg0907515920 NA 1.12E-07 mr1336_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
vg0907515920 9.42E-06 NA mr1338_2 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
vg0907515920 NA 1.63E-07 mr1338_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
vg0907515920 NA 6.62E-06 mr1355_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
vg0907515920 NA 1.97E-06 mr1360_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
vg0907515920 NA 2.33E-06 mr1360_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
vg0907515920 NA 4.22E-06 mr1371_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
vg0907515920 NA 5.55E-06 mr1449_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
vg0907515920 NA 9.35E-06 mr1452_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
vg0907515920 NA 8.73E-08 mr1482_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
vg0907515920 NA 2.96E-06 mr1527_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
vg0907515920 NA 6.99E-08 mr1540_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
vg0907515920 NA 6.58E-11 mr1565_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
vg0907515920 NA 2.58E-10 mr1715_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
vg0907515920 NA 1.50E-07 mr1717_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
vg0907515920 NA 6.25E-07 mr1727_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
vg0907515920 NA 2.28E-08 mr1732_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
vg0907515920 NA 8.09E-09 mr1861_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
vg0907515920 NA 2.05E-08 mr1895_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
vg0907515920 NA 3.08E-08 mr1895_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
vg0907515920 NA 3.69E-06 mr1946_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
vg0907515920 NA 3.69E-06 mr1948_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
vg0907515920 NA 5.31E-09 mr1977_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
vg0907515920 7.59E-06 7.59E-06 mr1991_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