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Detailed information for vg1117157515:

Variant ID: vg1117157515 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 17157515
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, A: 0.02, others allele: 0.00, population size: 63. )

Flanking Sequence (100 bp) in Reference Genome:


TGAAGGCAGCTACTCCATCCACGTCATCGTCATAACGATTTGGTGAATGACGGTGACCTCGTGCTGCACGGCACTGGTTGATCATGTCACGAAGGTCGAC[G/A]
GGACGCTGACGAGGTGGAGAACGAGGTCGTTCAGCTCGGCGCTCCCTGTGACGTTCGGGAAGCGAGTGAACAGATCGTTCGTCGTGACCCCTGCTCCTGC

Reverse complement sequence

GCAGGAGCAGGGGTCACGACGAACGATCTGTTCACTCGCTTCCCGAACGTCACAGGGAGCGCCGAGCTGAACGACCTCGTTCTCCACCTCGTCAGCGTCC[C/T]
GTCGACCTTCGTGACATGATCAACCAGTGCCGTGCAGCACGAGGTCACCGTCATTCACCAAATCGTTATGACGATGACGTGGATGGAGTAGCTGCCTTCA

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 35.90% 32.50% 3.49% 28.16% NA
All Indica  2759 30.20% 47.60% 4.64% 17.58% NA
All Japonica  1512 52.20% 8.10% 0.53% 39.15% NA
Aus  269 15.20% 21.90% 9.67% 53.16% NA
Indica I  595 16.80% 77.30% 1.68% 4.20% NA
Indica II  465 33.50% 28.40% 5.81% 32.26% NA
Indica III  913 36.00% 40.70% 6.13% 17.09% NA
Indica Intermediate  786 31.40% 44.50% 4.45% 19.59% NA
Temperate Japonica  767 85.30% 2.10% 0.26% 12.39% NA
Tropical Japonica  504 17.30% 16.70% 0.79% 65.28% NA
Japonica Intermediate  241 19.90% 9.50% 0.83% 69.71% NA
VI/Aromatic  96 5.20% 3.10% 2.08% 89.58% NA
Intermediate  90 31.10% 40.00% 1.11% 27.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1117157515 G -> A LOC_Os11g29570.1 synonymous_variant ; p.Pro334Pro; LOW synonymous_codon Average:26.26; most accessible tissue: Callus, score: 41.425 N N N N
vg1117157515 G -> DEL LOC_Os11g29570.1 N frameshift_variant Average:26.26; most accessible tissue: Callus, score: 41.425 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1117157515 NA 7.84E-06 mr1115 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
vg1117157515 NA 4.69E-08 mr1215 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
vg1117157515 NA 7.04E-10 mr1352 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
vg1117157515 7.09E-06 2.58E-07 mr1407 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
vg1117157515 NA 3.66E-11 mr1439 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
vg1117157515 NA 1.87E-06 mr1516 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
vg1117157515 NA 6.55E-07 mr1622 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
vg1117157515 NA 7.37E-14 mr1653 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
vg1117157515 1.48E-06 1.47E-06 mr1869 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
vg1117157515 3.25E-06 3.24E-06 mr1869 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
vg1117157515 NA 3.00E-07 mr1979 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
vg1117157515 NA 9.48E-06 mr1800_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