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Detailed information for vg0709033301:

Variant ID: vg0709033301 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 9033301
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTAGAGACATAGATGACACACATGCATAAGTTTGGAGGCTATTTGTGCACTTTACTCTTTCTTATAATATTTTTTTCTAATTTATTAGAGCGTTACATAA[C/T]
GATTTAGGAGCGTGTACAAGATGTTTAACGAAGTCATAGTATATAATAGATAGACAAATAAATAAATACTACTATATATCTTATAGGTGGAAGACATGCA

Reverse complement sequence

TGCATGTCTTCCACCTATAAGATATATAGTAGTATTTATTTATTTGTCTATCTATTATATACTATGACTTCGTTAAACATCTTGTACACGCTCCTAAATC[G/A]
TTATGTAACGCTCTAATAAATTAGAAAAAAATATTATAAGAAAGAGTAAAGTGCACAAATAGCCTCCAAACTTATGCATGTGTGTCATCTATGTCTCTAA

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 96.00% 3.40% 0.55% 0.00% NA
All Indica  2759 99.50% 0.40% 0.07% 0.00% NA
All Japonica  1512 98.90% 0.50% 0.60% 0.00% NA
Aus  269 41.30% 53.20% 5.58% 0.00% NA
Indica I  595 99.70% 0.00% 0.34% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 98.60% 1.40% 0.00% 0.00% NA
Temperate Japonica  767 99.70% 0.00% 0.26% 0.00% NA
Tropical Japonica  504 98.60% 0.20% 1.19% 0.00% NA
Japonica Intermediate  241 96.70% 2.90% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 98.90% 1.10% 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
vg0709033301 C -> T LOC_Os07g15580.1 upstream_gene_variant ; 3782.0bp to feature; MODIFIER silent_mutation Average:43.023; most accessible tissue: Callus, score: 73.014 N N N N
vg0709033301 C -> T LOC_Os07g15600.1 downstream_gene_variant ; 2659.0bp to feature; MODIFIER silent_mutation Average:43.023; most accessible tissue: Callus, score: 73.014 N N N N
vg0709033301 C -> T LOC_Os07g15590.1 intron_variant ; MODIFIER silent_mutation Average:43.023; most accessible tissue: Callus, score: 73.014 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0709033301 NA 1.33E-16 mr1240 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
vg0709033301 NA 8.53E-38 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
vg0709033301 4.58E-06 NA mr1098_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
vg0709033301 NA 1.36E-16 mr1113_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
vg0709033301 7.17E-06 NA mr1119_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
vg0709033301 1.95E-08 NA mr1123_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
vg0709033301 8.25E-06 8.88E-18 mr1240_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
vg0709033301 1.98E-07 NA mr1242_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
vg0709033301 2.29E-07 NA mr1247_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
vg0709033301 9.06E-06 NA mr1496_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
vg0709033301 NA 6.76E-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
vg0709033301 NA 5.71E-31 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
vg0709033301 NA 5.26E-47 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
vg0709033301 NA 3.08E-29 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
vg0709033301 NA 1.74E-06 mr1762_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
vg0709033301 4.69E-08 5.75E-15 mr1936_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