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Detailed information for vg1010015339:

Variant ID: vg1010015339 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 10015339
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.80, A: 0.20, others allele: 0.00, population size: 209. )

Flanking Sequence (100 bp) in Reference Genome:


GGAAGAAAATTTTATATTACCAGCCAGTCCAGTTCTCTGTCCACATTTTAGGGATGCTTGTCCTGTTTGAAAACCACTCATGGCAATAGAATCCATTACA[G/A]
GTGTTGACCTAAATTTGTCAGAAAAATGATGACATGCATTTCATTCAACCAAACAATGCAATAATAAACTTAAATATAGAATATTTTGAATTGCAATCGA

Reverse complement sequence

TCGATTGCAATTCAAAATATTCTATATTTAAGTTTATTATTGCATTGTTTGGTTGAATGAAATGCATGTCATCATTTTTCTGACAAATTTAGGTCAACAC[C/T]
TGTAATGGATTCTATTGCCATGAGTGGTTTTCAAACAGGACAAGCATCCCTAAAATGTGGACAGAGAACTGGACTGGCTGGTAATATAAAATTTTCTTCC

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 67.30% 32.60% 0.08% 0.00% NA
All Indica  2759 94.10% 5.80% 0.07% 0.00% NA
All Japonica  1512 33.10% 66.90% 0.00% 0.00% NA
Aus  269 1.90% 98.10% 0.00% 0.00% NA
Indica I  595 96.00% 3.90% 0.17% 0.00% NA
Indica II  465 97.20% 2.80% 0.00% 0.00% NA
Indica III  913 94.10% 5.90% 0.00% 0.00% NA
Indica Intermediate  786 91.00% 8.90% 0.13% 0.00% NA
Temperate Japonica  767 12.40% 87.60% 0.00% 0.00% NA
Tropical Japonica  504 62.30% 37.70% 0.00% 0.00% NA
Japonica Intermediate  241 38.20% 61.80% 0.00% 0.00% NA
VI/Aromatic  96 37.50% 61.50% 1.04% 0.00% NA
Intermediate  90 46.70% 52.20% 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
vg1010015339 G -> A LOC_Os10g19960.1 synonymous_variant ; p.Thr237Thr; LOW synonymous_codon Average:51.138; most accessible tissue: Zhenshan97 panicle, score: 65.386 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1010015339 NA 2.55E-06 mr1177 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
vg1010015339 NA 6.29E-15 mr1199 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
vg1010015339 5.81E-06 5.81E-06 mr1260 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
vg1010015339 3.26E-07 5.69E-10 mr1261 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
vg1010015339 NA 7.29E-07 mr1495 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
vg1010015339 NA 5.66E-07 mr1763 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
vg1010015339 NA 1.40E-06 mr1110_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
vg1010015339 NA 9.43E-18 mr1180_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
vg1010015339 NA 2.73E-21 mr1183_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
vg1010015339 NA 1.16E-08 mr1495_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
vg1010015339 NA 2.31E-10 mr1649_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