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Detailed information for vg0113034093:

Variant ID: vg0113034093 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 13034093
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 108. )

Flanking Sequence (100 bp) in Reference Genome:


GCCGGAGAACCAAACTGGGAGGAATTTACCACAGCCTTCCGTGACAACTTCGTGCCTGCTGCGGTGATGCGGATGAAGAAGAATGAGTTCAGGAGACTAC[A/G]
GCAAGGGAATACCACAGTACAAGAGTACCTGAACCGTTTCACTCAGCTGGCGCGCTACGCGACTAGAGATCTTGCCGACGAGGAGGAAAAGATCGACAAA

Reverse complement sequence

TTTGTCGATCTTTTCCTCCTCGTCGGCAAGATCTCTAGTCGCGTAGCGCGCCAGCTGAGTGAAACGGTTCAGGTACTCTTGTACTGTGGTATTCCCTTGC[T/C]
GTAGTCTCCTGAACTCATTCTTCTTCATCCGCATCACCGCAGCAGGCACGAAGTTGTCACGGAAGGCTGTGGTAAATTCCTCCCAGTTTGGTTCTCCGGC

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 44.90% 44.20% 7.43% 3.39% NA
All Indica  2759 66.20% 27.10% 6.27% 0.47% NA
All Japonica  1512 11.20% 77.70% 1.39% 9.66% NA
Aus  269 27.10% 28.60% 44.24% 0.00% NA
Indica I  595 35.00% 50.60% 13.28% 1.18% NA
Indica II  465 60.40% 33.30% 5.38% 0.86% NA
Indica III  913 93.50% 4.70% 1.75% 0.00% NA
Indica Intermediate  786 61.50% 31.60% 6.74% 0.25% NA
Temperate Japonica  767 18.00% 80.70% 0.39% 0.91% NA
Tropical Japonica  504 5.20% 64.90% 3.17% 26.79% NA
Japonica Intermediate  241 2.50% 95.00% 0.83% 1.66% NA
VI/Aromatic  96 30.20% 32.30% 37.50% 0.00% NA
Intermediate  90 28.90% 67.80% 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
vg0113034093 A -> G LOC_Os01g23200.1 missense_variant ; p.Gln124Arg; MODERATE nonsynonymous_codon ; Q124W Average:7.868; most accessible tissue: Minghui63 panicle, score: 16.27 probably damaging 2.97 DELETERIOUS 0.00
vg0113034093 A -> G LOC_Os01g23200.1 missense_variant ; p.Gln124Arg; MODERATE nonsynonymous_codon ; Q124R Average:7.868; most accessible tissue: Minghui63 panicle, score: 16.27 benign -0.436 TOLERATED 0.64
vg0113034093 A -> DEL LOC_Os01g23200.1 N frameshift_variant Average:7.868; most accessible tissue: Minghui63 panicle, score: 16.27 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0113034093 NA 3.67E-11 Plant_height Jap_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0113034093 NA 2.01E-06 mr1164 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
vg0113034093 NA 1.04E-09 mr1648 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
vg0113034093 NA 4.19E-09 mr1648 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
vg0113034093 NA 8.76E-22 mr1010_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
vg0113034093 NA 3.04E-09 mr1030_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
vg0113034093 NA 2.84E-06 mr1030_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
vg0113034093 NA 2.92E-13 mr1035_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
vg0113034093 1.56E-07 2.36E-11 mr1164_2 Jap_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
vg0113034093 NA 4.05E-06 mr1380_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
vg0113034093 NA 2.02E-06 mr1561_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
vg0113034093 NA 2.19E-09 mr1576_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
vg0113034093 NA 4.23E-09 mr1709_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
vg0113034093 NA 4.20E-06 mr1875_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