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Detailed information for vg0315349538:

Variant ID: vg0315349538 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 15349538
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:


ATCGGCTTATTCTTTGCCGACAAGATTCAGTGCCGAGGAGAAATCACATCCACTCTAATGATGGATCGGCTACTTAACCTACCAGGACCCTCTCTGGGCA[G/A]
TATTGATAATATTAAGTTGGCAGGATTTAGAAGCAAAAACTTTGACAGATGGTGGGGTAAATGGAAGCTGCATCTATTTCATCAATCAGCCTCAATGTAC

Reverse complement sequence

GTACATTGAGGCTGATTGATGAAATAGATGCAGCTTCCATTTACCCCACCATCTGTCAAAGTTTTTGCTTCTAAATCCTGCCAACTTAATATTATCAATA[C/T]
TGCCCAGAGAGGGTCCTGGTAGGTTAAGTAGCCGATCCATCATTAGAGTGGATGTGATTTCTCCTCGGCACTGAATCTTGTCGGCAAAGAATAAGCCGAT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 93.70% 6.00% 0.30% 0.00% NA
All Indica  2759 95.80% 4.20% 0.00% 0.00% NA
All Japonica  1512 93.30% 6.00% 0.73% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 93.30% 6.70% 0.00% 0.00% NA
Indica III  913 91.70% 8.30% 0.00% 0.00% NA
Indica Intermediate  786 99.00% 1.00% 0.00% 0.00% NA
Temperate Japonica  767 95.80% 3.10% 1.04% 0.00% NA
Tropical Japonica  504 92.90% 6.90% 0.20% 0.00% NA
Japonica Intermediate  241 86.30% 12.90% 0.83% 0.00% NA
VI/Aromatic  96 20.80% 76.00% 3.12% 0.00% NA
Intermediate  90 93.30% 6.70% 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
vg0315349538 G -> A LOC_Os03g26880.1 missense_variant ; p.Ser355Asn; MODERATE nonsynonymous_codon ; S355N Average:36.161; most accessible tissue: Zhenshan97 flag leaf, score: 48.165 benign 0.3 TOLERATED 0.05

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0315349538 6.68E-06 6.68E-06 mr1098 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
vg0315349538 8.65E-06 8.65E-06 mr1099 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
vg0315349538 NA 8.26E-06 mr1101 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
vg0315349538 NA 1.36E-06 mr1441 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
vg0315349538 1.20E-07 1.20E-07 mr1855 Jap_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
vg0315349538 NA 1.46E-07 mr1962 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
vg0315349538 NA 6.04E-07 mr1057_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
vg0315349538 NA 1.55E-07 mr1167_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
vg0315349538 NA 3.63E-06 mr1726_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
vg0315349538 3.00E-06 3.00E-06 mr1950_2 Jap_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
vg0315349538 8.11E-06 8.11E-06 mr1981_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