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Detailed information for vg0523519263:

Variant ID: vg0523519263 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 23519263
Reference Allele: CAlternative Allele: G
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.93, G: 0.08, others allele: 0.00, population size: 218. )

Flanking Sequence (100 bp) in Reference Genome:


GCTCCATTTGTGTTACCAGGTAAACATAACCTATAGCAATCCAAATGGTGTAGAAATTACAGTAAAATCTGGGAAGGGGCAGTGTTCCTTACACACCAAG[C/G]
AAACAGTTTTTGATTGGCAACAACAGTTTCAGCAGTTTGCAGCTTATGCAACACGCGCGAATCCAATCTACGGAGCCTCCTTCCTTGTTTTCACTGTTGT

Reverse complement sequence

ACAACAGTGAAAACAAGGAAGGAGGCTCCGTAGATTGGATTCGCGCGTGTTGCATAAGCTGCAAACTGCTGAAACTGTTGTTGCCAATCAAAAACTGTTT[G/C]
CTTGGTGTGTAAGGAACACTGCCCCTTCCCAGATTTTACTGTAATTTCTACACCATTTGGATTGCTATAGGTTATGTTTACCTGGTAACACAAATGGAGC

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 62.60% 36.90% 0.30% 0.21% NA
All Indica  2759 94.80% 4.60% 0.29% 0.29% NA
All Japonica  1512 0.40% 99.30% 0.26% 0.07% NA
Aus  269 94.40% 5.60% 0.00% 0.00% NA
Indica I  595 97.60% 1.50% 0.34% 0.50% NA
Indica II  465 93.80% 6.00% 0.00% 0.22% NA
Indica III  913 92.60% 7.00% 0.33% 0.11% NA
Indica Intermediate  786 95.90% 3.30% 0.38% 0.38% NA
Temperate Japonica  767 0.40% 99.50% 0.13% 0.00% NA
Tropical Japonica  504 0.60% 99.00% 0.40% 0.00% NA
Japonica Intermediate  241 0.00% 99.20% 0.41% 0.41% NA
VI/Aromatic  96 36.50% 63.50% 0.00% 0.00% NA
Intermediate  90 52.20% 44.40% 2.22% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0523519263 C -> DEL LOC_Os05g40040.1 N frameshift_variant Average:62.318; most accessible tissue: Minghui63 panicle, score: 82.797 N N N N
vg0523519263 C -> G LOC_Os05g40040.1 missense_variant ; p.Gln243Glu; MODERATE nonsynonymous_codon ; Q243E Average:62.318; most accessible tissue: Minghui63 panicle, score: 82.797 unknown unknown TOLERATED 0.10

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0523519263 NA 1.92E-46 mr1136 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
vg0523519263 NA 1.38E-27 mr1238 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
vg0523519263 NA 3.61E-31 mr1243 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
vg0523519263 NA 1.77E-30 mr1309 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
vg0523519263 NA 4.87E-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
vg0523519263 NA 5.19E-22 mr1548 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
vg0523519263 NA 2.13E-11 mr1609 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
vg0523519263 NA 1.31E-38 mr1828 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
vg0523519263 NA 3.31E-23 mr1841 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
vg0523519263 NA 1.19E-07 mr1915 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
vg0523519263 9.10E-07 NA mr1940 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
vg0523519263 NA 4.92E-18 mr1968 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
vg0523519263 NA 3.20E-28 mr1238_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
vg0523519263 NA 1.80E-25 mr1484_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
vg0523519263 NA 2.30E-67 mr1828_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
vg0523519263 NA 1.55E-31 mr1841_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
vg0523519263 NA 2.08E-20 mr1900_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
vg0523519263 NA 1.02E-06 mr1915_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
vg0523519263 NA 4.41E-21 mr1968_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