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Detailed information for vg0815339015:

Variant ID: vg0815339015 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 15339015
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.97, C: 0.02, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:


GGACCTGTAAGCATCTTCCTGCTTTGATTGCTCTAGTTACTATTGTCCTGTTAGGTAATAAAGTGCACGTTAGTATTATGATAAGTTGTAGTAACGTTAG[T/C]
GAGAGAAATAAAATTCAGTTTACCTTCGTTTCACAAGTCATGTTTACATTTTGATTTATATAGGACTCTTCGTTATGATTTGATACATGCTCCCTGGGAT

Reverse complement sequence

ATCCCAGGGAGCATGTATCAAATCATAACGAAGAGTCCTATATAAATCAAAATGTAAACATGACTTGTGAAACGAAGGTAAACTGAATTTTATTTCTCTC[A/G]
CTAACGTTACTACAACTTATCATAATACTAACGTGCACTTTATTACCTAACAGGACAATAGTAACTAGAGCAATCAAAGCAGGAAGATGCTTACAGGTCC

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 90.50% 8.60% 0.25% 0.57% NA
All Indica  2759 99.50% 0.10% 0.40% 0.00% NA
All Japonica  1512 75.70% 22.50% 0.00% 1.79% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 97.80% 0.20% 1.94% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 99.60% 0.10% 0.25% 0.00% NA
Temperate Japonica  767 87.70% 9.50% 0.00% 2.74% NA
Tropical Japonica  504 52.60% 46.60% 0.00% 0.79% NA
Japonica Intermediate  241 85.90% 13.30% 0.00% 0.83% NA
VI/Aromatic  96 45.80% 54.20% 0.00% 0.00% NA
Intermediate  90 84.40% 14.40% 1.11% 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
vg0815339015 T -> C LOC_Os08g25240.1 upstream_gene_variant ; 3638.0bp to feature; MODIFIER silent_mutation Average:24.413; most accessible tissue: Callus, score: 40.15 N N N N
vg0815339015 T -> C LOC_Os08g25250.1 intron_variant ; MODIFIER silent_mutation Average:24.413; most accessible tissue: Callus, score: 40.15 N N N N
vg0815339015 T -> DEL N N silent_mutation Average:24.413; most accessible tissue: Callus, score: 40.15 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0815339015 NA 9.04E-06 mr1041 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
vg0815339015 NA 1.78E-06 mr1092 Jap_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
vg0815339015 NA 1.23E-06 mr1184 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
vg0815339015 NA 9.00E-06 mr1616 Jap_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
vg0815339015 NA 3.18E-07 mr1680 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
vg0815339015 NA 9.38E-07 mr1709 Jap_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
vg0815339015 NA 2.15E-09 mr1746 Jap_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
vg0815339015 NA 3.74E-07 mr1835 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
vg0815339015 NA 2.09E-08 mr1851 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
vg0815339015 NA 1.92E-06 mr1851 Jap_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
vg0815339015 4.66E-06 1.55E-14 mr1864 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
vg0815339015 NA 1.20E-09 mr1864 Jap_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
vg0815339015 NA 7.08E-06 mr1194_2 Jap_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
vg0815339015 NA 7.06E-07 mr1671_2 Jap_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
vg0815339015 NA 3.61E-08 mr1805_2 Jap_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