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Detailed information for vg0114209645:

Variant ID: vg0114209645 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 14209645
Reference Allele: GAlternative Allele: C
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.76, C: 0.26, others allele: 0.00, population size: 82. )

Flanking Sequence (100 bp) in Reference Genome:


CAAATTTCCTACATATTAATGTGATATAGAAAGCCCATGAGAATGCATGGTTGCAGTGTGTTATACATCAATGTAAATATGGGTACCACACTTTAAATAT[G/C]
TGAATGGGTAAAGTCCTGGGGGACATATCCGGTGAAAATAAGCTGAGTGTTAGAAACTCGTGAAAATTATACCTAGAAGTTTTATAAATTCATGAAAAAA

Reverse complement sequence

TTTTTTCATGAATTTATAAAACTTCTAGGTATAATTTTCACGAGTTTCTAACACTCAGCTTATTTTCACCGGATATGTCCCCCAGGACTTTACCCATTCA[C/G]
ATATTTAAAGTGTGGTACCCATATTTACATTGATGTATAACACACTGCAACCATGCATTCTCATGGGCTTTCTATATCACATTAATATGTAGGAAATTTG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 34.10% 33.00% 0.34% 32.59% NA
All Indica  2759 2.40% 48.70% 0.43% 48.50% NA
All Japonica  1512 95.40% 4.50% 0.00% 0.13% NA
Aus  269 1.50% 33.10% 1.49% 63.94% NA
Indica I  595 2.70% 41.80% 0.84% 54.62% NA
Indica II  465 4.10% 24.90% 0.43% 70.54% NA
Indica III  913 0.50% 67.30% 0.22% 31.98% NA
Indica Intermediate  786 3.30% 46.30% 0.38% 50.00% NA
Temperate Japonica  767 98.40% 1.60% 0.00% 0.00% NA
Tropical Japonica  504 89.50% 10.30% 0.00% 0.20% NA
Japonica Intermediate  241 97.90% 1.70% 0.00% 0.41% NA
VI/Aromatic  96 54.20% 44.80% 0.00% 1.04% NA
Intermediate  90 52.20% 17.80% 0.00% 30.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0114209645 G -> DEL N N silent_mutation Average:22.295; most accessible tissue: Zhenshan97 panicle, score: 54.901 N N N N
vg0114209645 G -> C LOC_Os01g25160.1 downstream_gene_variant ; 834.0bp to feature; MODIFIER silent_mutation Average:22.295; most accessible tissue: Zhenshan97 panicle, score: 54.901 N N N N
vg0114209645 G -> C LOC_Os01g25150-LOC_Os01g25160 intergenic_region ; MODIFIER silent_mutation Average:22.295; most accessible tissue: Zhenshan97 panicle, score: 54.901 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0114209645 NA 2.37E-07 mr1090 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
vg0114209645 NA 1.12E-07 mr1110 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
vg0114209645 NA 1.09E-07 mr1121 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
vg0114209645 4.73E-06 1.85E-08 mr1193 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
vg0114209645 NA 5.30E-06 mr1200 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
vg0114209645 NA 3.28E-06 mr1211 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
vg0114209645 1.14E-06 1.96E-06 mr1229 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
vg0114209645 NA 1.14E-07 mr1244 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
vg0114209645 NA 8.17E-06 mr1298 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
vg0114209645 NA 3.44E-10 mr1458 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
vg0114209645 NA 9.82E-06 mr1676 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
vg0114209645 NA 1.05E-06 mr1677 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
vg0114209645 NA 4.38E-07 mr1677 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
vg0114209645 NA 1.60E-07 mr1218_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
vg0114209645 4.39E-06 NA mr1519_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
vg0114209645 NA 4.70E-12 mr1519_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