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Detailed information for vg0815712004:

Variant ID: vg0815712004 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 15712004
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, C: 0.01, others allele: 0.00, population size: 163. )

Flanking Sequence (100 bp) in Reference Genome:


TCCAAATTCCAAGTGATAGCCTCTCCTAGAACTCTTCCGTTGTTACAGTGATTTTTAATTTAGACTGATGCAATGAATTACTTATCTAGTTTTCATTGGA[T/C]
GGAAAAGCTAAAATCTCAATTGTGCAGTCATGATAATTAAGTTGGTATCTGTCCTACTGGTAACTCTAAACTGTCGGTTTCAGTTTCAACTAATGAACTA

Reverse complement sequence

TAGTTCATTAGTTGAAACTGAAACCGACAGTTTAGAGTTACCAGTAGGACAGATACCAACTTAATTATCATGACTGCACAATTGAGATTTTAGCTTTTCC[A/G]
TCCAATGAAAACTAGATAAGTAATTCATTGCATCAGTCTAAATTAAAAATCACTGTAACAACGGAAGAGTTCTAGGAGAGGCTATCACTTGGAATTTGGA

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 61.20% 38.60% 0.21% 0.00% NA
All Indica  2759 89.20% 10.50% 0.25% 0.00% NA
All Japonica  1512 18.90% 81.00% 0.07% 0.00% NA
Aus  269 40.10% 59.90% 0.00% 0.00% NA
Indica I  595 99.80% 0.00% 0.17% 0.00% NA
Indica II  465 95.50% 4.50% 0.00% 0.00% NA
Indica III  913 81.50% 18.20% 0.33% 0.00% NA
Indica Intermediate  786 86.50% 13.10% 0.38% 0.00% NA
Temperate Japonica  767 3.10% 96.90% 0.00% 0.00% NA
Tropical Japonica  504 27.80% 72.00% 0.20% 0.00% NA
Japonica Intermediate  241 50.60% 49.40% 0.00% 0.00% NA
VI/Aromatic  96 2.10% 97.90% 0.00% 0.00% NA
Intermediate  90 40.00% 57.80% 2.22% 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
vg0815712004 T -> C LOC_Os08g25820.1 intron_variant ; MODIFIER silent_mutation Average:48.723; most accessible tissue: Callus, score: 78.769 N N N N
vg0815712004 T -> C LOC_Os08g25820.2 intron_variant ; MODIFIER silent_mutation Average:48.723; most accessible tissue: Callus, score: 78.769 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0815712004 NA 1.59E-08 mr1238 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
vg0815712004 NA 7.25E-06 mr1309 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
vg0815712004 NA 3.96E-06 mr1519 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
vg0815712004 NA 1.63E-06 mr1841 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
vg0815712004 NA 6.94E-06 mr1064_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
vg0815712004 9.72E-09 3.04E-12 mr1238_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
vg0815712004 1.79E-08 2.56E-12 mr1484_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
vg0815712004 NA 7.26E-06 mr1519_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
vg0815712004 NA 5.17E-06 mr1609_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
vg0815712004 2.25E-07 1.67E-11 mr1841_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
vg0815712004 3.07E-06 1.01E-08 mr1900_2 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
vg0815712004 2.17E-07 2.17E-07 mr1945_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