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Detailed information for vg1018616939:

Variant ID: vg1018616939 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 18616939
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.94, A: 0.05, others allele: 0.00, population size: 182. )

Flanking Sequence (100 bp) in Reference Genome:


CTTGTGTACGACAACTGTGCTACCTGCATTTCAATTTGTTAGTATCAAATAAAGTGTTGTGACATGCATTTTTCTATGTTACTTGTTTATTCAAATTACC[G/A]
GTGTAGTATGTGACTTAAGCATGGTTAACTCATCATGTAGTAATGCTGGGCTTTGTGGCGATTGGGTTGTGCCGATTCCTGTGAATTGAAAAGCATGATG

Reverse complement sequence

CATCATGCTTTTCAATTCACAGGAATCGGCACAACCCAATCGCCACAAAGCCCAGCATTACTACATGATGAGTTAACCATGCTTAAGTCACATACTACAC[C/T]
GGTAATTTGAATAAACAAGTAACATAGAAAAATGCATGTCACAACACTTTATTTGATACTAACAAATTGAAATGCAGGTAGCACAGTTGTCGTACACAAG

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 45.40% 31.50% 2.48% 20.59% NA
All Indica  2759 73.00% 3.40% 2.86% 20.70% NA
All Japonica  1512 1.70% 87.50% 0.73% 10.05% NA
Aus  269 24.90% 1.90% 5.95% 67.29% NA
Indica I  595 81.00% 3.50% 4.20% 11.26% NA
Indica II  465 74.00% 2.20% 2.15% 21.72% NA
Indica III  913 72.10% 3.00% 1.42% 23.55% NA
Indica Intermediate  786 67.40% 4.70% 3.94% 23.92% NA
Temperate Japonica  767 1.30% 96.20% 0.13% 2.35% NA
Tropical Japonica  504 2.60% 73.80% 1.79% 21.83% NA
Japonica Intermediate  241 1.20% 88.40% 0.41% 9.96% NA
VI/Aromatic  96 3.10% 45.80% 3.12% 47.92% NA
Intermediate  90 40.00% 25.60% 8.89% 25.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1018616939 G -> A LOC_Os10g34884.1 missense_variant&splice_region_variant ; p.Pro261Leu; MODERATE nonsynonymous_codon ; P261L Average:34.205; most accessible tissue: Callus, score: 61.326 unknown unknown TOLERATED 0.31
vg1018616939 G -> DEL LOC_Os10g34884.1 N frameshift_variant Average:34.205; most accessible tissue: Callus, score: 61.326 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1018616939 NA 6.48E-17 mr1484 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
vg1018616939 NA 1.23E-38 mr1784 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
vg1018616939 NA 5.73E-14 mr1909 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
vg1018616939 7.82E-07 1.10E-06 mr1925 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
vg1018616939 NA 1.41E-10 mr1945 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
vg1018616939 NA 1.04E-12 mr1217_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
vg1018616939 NA 6.86E-52 mr1261_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
vg1018616939 NA 1.78E-06 mr1275_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
vg1018616939 NA 4.51E-14 mr1575_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
vg1018616939 NA 7.00E-12 mr1641_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
vg1018616939 NA 2.34E-25 mr1653_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
vg1018616939 NA 1.63E-10 mr1667_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
vg1018616939 NA 8.22E-11 mr1714_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
vg1018616939 NA 1.02E-19 mr1731_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
vg1018616939 NA 3.69E-16 mr1767_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
vg1018616939 NA 5.09E-13 mr1838_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
vg1018616939 NA 2.79E-08 mr1909_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
vg1018616939 NA 8.77E-08 mr1921_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