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Detailed information for vg1104596397:

Variant ID: vg1104596397 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 4596397
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.58, T: 0.42, others allele: 0.00, population size: 92. )

Flanking Sequence (100 bp) in Reference Genome:


GAATTTTTCAAATTTCAACTATTTCCTAATTGTATTTTTATGTGGACTCTATACTTTACTTCTAATATTCCTTATTTTTAATTCCGAATTTCAGTTATTT[C/T]
CTAATTGTATTTCTATATGGATTCTTATCCCCTCTTCTAATATTCCTTATTTTTAATTCCGAATTTTAACTATTAAATTGTGTTTCTATATGGACTCTGG

Reverse complement sequence

CCAGAGTCCATATAGAAACACAATTTAATAGTTAAAATTCGGAATTAAAAATAAGGAATATTAGAAGAGGGGATAAGAATCCATATAGAAATACAATTAG[G/A]
AAATAACTGAAATTCGGAATTAAAAATAAGGAATATTAGAAGTAAAGTATAGAGTCCACATAAAAATACAATTAGGAAATAGTTGAAATTTGAAAAATTC

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 78.80% 0.70% 20.38% 0.19% NA
All Indica  2759 87.00% 0.40% 12.47% 0.14% NA
All Japonica  1512 71.60% 0.90% 27.18% 0.33% NA
Aus  269 34.20% 2.60% 63.20% 0.00% NA
Indica I  595 59.80% 1.00% 38.49% 0.67% NA
Indica II  465 96.80% 0.20% 3.01% 0.00% NA
Indica III  913 94.90% 0.10% 5.04% 0.00% NA
Indica Intermediate  786 92.70% 0.30% 7.00% 0.00% NA
Temperate Japonica  767 54.20% 1.40% 43.68% 0.65% NA
Tropical Japonica  504 95.00% 0.00% 4.96% 0.00% NA
Japonica Intermediate  241 78.00% 0.80% 21.16% 0.00% NA
VI/Aromatic  96 71.90% 1.00% 27.08% 0.00% NA
Intermediate  90 86.70% 0.00% 13.33% 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
vg1104596397 C -> T LOC_Os11g08640.1 upstream_gene_variant ; 1113.0bp to feature; MODIFIER silent_mutation Average:15.525; most accessible tissue: Minghui63 panicle, score: 29.741 N N N N
vg1104596397 C -> T LOC_Os11g08630-LOC_Os11g08640 intergenic_region ; MODIFIER silent_mutation Average:15.525; most accessible tissue: Minghui63 panicle, score: 29.741 N N N N
vg1104596397 C -> DEL N N silent_mutation Average:15.525; most accessible tissue: Minghui63 panicle, score: 29.741 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1104596397 NA 1.27E-06 mr1201 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
vg1104596397 NA 1.20E-07 mr1274 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
vg1104596397 NA 4.15E-11 mr1274 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
vg1104596397 1.19E-07 1.19E-07 mr1337 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
vg1104596397 3.43E-06 3.44E-06 mr1381 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
vg1104596397 9.27E-07 1.17E-07 mr1484 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
vg1104596397 7.94E-07 7.94E-07 mr1487 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
vg1104596397 8.02E-07 NA mr1500 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
vg1104596397 NA 9.91E-07 mr1526 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
vg1104596397 3.78E-06 NA mr1549 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
vg1104596397 3.16E-06 3.16E-06 mr1572 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
vg1104596397 1.19E-07 5.71E-10 mr1638 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
vg1104596397 7.28E-06 NA mr1923 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
vg1104596397 6.58E-07 3.95E-06 mr1923 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
vg1104596397 6.00E-07 2.59E-09 mr1933 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
vg1104596397 8.33E-06 8.33E-06 mr1954 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
vg1104596397 NA 6.81E-06 mr1397_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
vg1104596397 NA 2.08E-06 mr1608_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