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Detailed information for vg1017949223:

Variant ID: vg1017949223 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 17949223
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.68, A: 0.33, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:


GGATCAGTGTACCTTAATCCACTCAATGAAAAGGATTTTCTTTTACCAAGAGATCATAATGGCATCAGATAACCAAATTAAGAAAGCACCATTTTTTGTC[A/G]
TCTGCGAGAAAGACAATGTACATACCTAGCAAACAGCCAGATCGCCCTCGCAGTCGCCGCCCAAACAAACACACACGAACTCGTCGCGTTTATCTCAACT

Reverse complement sequence

AGTTGAGATAAACGCGACGAGTTCGTGTGTGTTTGTTTGGGCGGCGACTGCGAGGGCGATCTGGCTGTTTGCTAGGTATGTACATTGTCTTTCTCGCAGA[T/C]
GACAAAAAATGGTGCTTTCTTAATTTGGTTATCTGATGCCATTATGATCTCTTGGTAAAAGAAAATCCTTTTCATTGAGTGGATTAAGGTACACTGATCC

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 62.00% 37.70% 0.06% 0.28% NA
All Indica  2759 91.10% 8.50% 0.07% 0.29% NA
All Japonica  1512 23.20% 76.50% 0.00% 0.33% NA
Aus  269 2.60% 97.40% 0.00% 0.00% NA
Indica I  595 95.50% 4.50% 0.00% 0.00% NA
Indica II  465 86.50% 12.50% 0.22% 0.86% NA
Indica III  913 92.10% 7.70% 0.11% 0.11% NA
Indica Intermediate  786 89.40% 10.20% 0.00% 0.38% NA
Temperate Japonica  767 2.60% 97.10% 0.00% 0.26% NA
Tropical Japonica  504 42.70% 57.10% 0.00% 0.20% NA
Japonica Intermediate  241 48.10% 51.00% 0.00% 0.83% NA
VI/Aromatic  96 4.20% 95.80% 0.00% 0.00% NA
Intermediate  90 58.90% 40.00% 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
vg1017949223 A -> G LOC_Os10g33830.1 intron_variant ; MODIFIER silent_mutation Average:62.882; most accessible tissue: Callus, score: 93.384 N N N N
vg1017949223 A -> DEL N N silent_mutation Average:62.882; most accessible tissue: Callus, score: 93.384 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1017949223 NA 1.02E-07 mr1053 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
vg1017949223 NA 2.94E-06 mr1058 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
vg1017949223 NA 2.31E-11 mr1883 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
vg1017949223 6.37E-06 6.37E-06 mr1929 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
vg1017949223 NA 1.13E-06 mr1045_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
vg1017949223 NA 9.56E-07 mr1053_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
vg1017949223 NA 3.15E-16 mr1147_2 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
vg1017949223 NA 7.69E-07 mr1222_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
vg1017949223 NA 3.17E-27 mr1270_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
vg1017949223 NA 1.36E-23 mr1316_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
vg1017949223 NA 5.55E-06 mr1624_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
vg1017949223 NA 8.85E-12 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
vg1017949223 NA 1.13E-15 mr1744_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
vg1017949223 NA 6.82E-06 mr1751_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
vg1017949223 NA 4.02E-06 mr1788_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
vg1017949223 NA 2.21E-06 mr1925_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
vg1017949223 NA 7.44E-06 mr1929_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