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Detailed information for vg0613088823:

Variant ID: vg0613088823 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 13088823
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 272. )

Flanking Sequence (100 bp) in Reference Genome:


CCATCTTGTCCCGAAAATTTGGAGAAGTCCGGGACTTTGAACCGATTGGGAAGAGGAACTCTCTCAAACCACTCAGGGTAAGGCTGCCGATACAAGCTTC[C/T]
AGTCTCTTTTGGTTTAAGCCCAAACTGTTCCCTCATTACGTCGGCAATCACATCGGCCCATGGTCGCTGCTGAGCTGCTGCTTGTGGCTGTTGCTGCATG

Reverse complement sequence

CATGCAGCAACAGCCACAAGCAGCAGCTCAGCAGCGACCATGGGCCGATGTGATTGCCGACGTAATGAGGGAACAGTTTGGGCTTAAACCAAAAGAGACT[G/A]
GAAGCTTGTATCGGCAGCCTTACCCTGAGTGGTTTGAGAGAGTTCCTCTTCCCAATCGGTTCAAAGTCCCGGACTTCTCCAAATTTTCGGGACAAGATGG

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 90.60% 9.30% 0.06% 0.00% NA
All Indica  2759 85.70% 14.30% 0.04% 0.00% NA
All Japonica  1512 99.10% 0.90% 0.07% 0.00% NA
Aus  269 88.80% 10.80% 0.37% 0.00% NA
Indica I  595 87.10% 12.80% 0.17% 0.00% NA
Indica II  465 98.70% 1.30% 0.00% 0.00% NA
Indica III  913 80.60% 19.40% 0.00% 0.00% NA
Indica Intermediate  786 82.80% 17.20% 0.00% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 97.80% 2.20% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.40% 0.41% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 96.70% 3.30% 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
vg0613088823 C -> T LOC_Os06g22520.1 missense_variant ; p.Gly391Arg; MODERATE nonsynonymous_codon ; G391R Average:47.756; most accessible tissue: Zhenshan97 flag leaf, score: 68.25 benign 0.92 DELETERIOUS 0.04

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0613088823 NA 1.58E-06 mr1042 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
vg0613088823 NA 7.09E-07 mr1043 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
vg0613088823 NA 3.64E-06 mr1043 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
vg0613088823 NA 6.15E-07 mr1912 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
vg0613088823 NA 5.47E-06 mr1912 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
vg0613088823 NA 9.68E-07 mr1043_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
vg0613088823 NA 3.61E-06 mr1291_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
vg0613088823 NA 4.68E-06 mr1291_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
vg0613088823 NA 1.49E-06 mr1677_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
vg0613088823 3.60E-06 NA mr1860_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
vg0613088823 NA 3.99E-06 mr1860_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