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Detailed information for vg1117954021:

Variant ID: vg1117954021 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 17954021
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:


GCCACAGCACCGATTTTGTCCAACACCTGACAGGGGCCAAAGTAGCGAAAAGCTAACTTGTGATTAGTGCGGACAGCTAGCGAAGTCTGGGCATAAGGCT[G/A]
CGCCTTCAAAAACACCCAATCACCAATGCAAAACACTCTATCAGAGCAATGTTTATCAGCTTGATCTTTCATTCGTTGCTGGGCACGGAGGAGATGCTGA

Reverse complement sequence

TCAGCATCTCCTCCGTGCCCAGCAACGAATGAAAGATCAAGCTGATAAACATTGCTCTGATAGAGTGTTTTGCATTGGTGATTGGGTGTTTTTGAAGGCG[C/T]
AGCCTTATGCCCAGACTTCGCTAGCTGTCCGCACTAATCACAAGTTAGCTTTTCGCTACTTTGGCCCCTGTCAGGTGTTGGACAAAATCGGTGCTGTGGC

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 82.00% 5.50% 0.78% 11.70% NA
All Indica  2759 93.70% 0.20% 0.36% 5.76% NA
All Japonica  1512 60.20% 16.00% 1.59% 22.22% NA
Aus  269 98.50% 0.40% 0.00% 1.12% NA
Indica I  595 92.30% 0.00% 0.84% 6.89% NA
Indica II  465 99.60% 0.00% 0.00% 0.43% NA
Indica III  913 91.00% 0.00% 0.44% 8.54% NA
Indica Intermediate  786 94.30% 0.80% 0.13% 4.83% NA
Temperate Japonica  767 94.90% 2.20% 1.17% 1.69% NA
Tropical Japonica  504 16.90% 41.10% 2.18% 39.88% NA
Japonica Intermediate  241 40.20% 7.50% 1.66% 50.62% NA
VI/Aromatic  96 45.80% 3.10% 1.04% 50.00% NA
Intermediate  90 82.20% 7.80% 2.22% 7.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1117954021 G -> A LOC_Os11g30840.1 stop_gained ; p.Gln769*; HIGH stop_gained Average:66.04; most accessible tissue: Zhenshan97 flag leaf, score: 79.71 N N N N
vg1117954021 G -> DEL LOC_Os11g30840.1 N frameshift_variant Average:66.04; most accessible tissue: Zhenshan97 flag leaf, score: 79.71 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1117954021 NA 9.57E-07 mr1676 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
vg1117954021 NA 7.56E-08 mr1951 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
vg1117954021 NA 9.08E-06 mr1398_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
vg1117954021 NA 9.99E-08 mr1401_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
vg1117954021 4.25E-06 NA mr1676_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
vg1117954021 NA 4.62E-07 mr1696_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