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Detailed information for vg1101999349:

Variant ID: vg1101999349 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 1999349
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.89, A: 0.12, others allele: 0.00, population size: 227. )

Flanking Sequence (100 bp) in Reference Genome:


GGCGACAAGCTTAGGAAGATGCCGTGCGCTGATTCGCACTGCTTCCATGAGCAGTGCATATTCAGCTGGCTTCTGATTAACCGCCATTGCCCGCTCTGCC[G/A]
CTTCCCGTTGCCTGCTGAGACGGAGGAGGATGAAGAGGTGGTCCAGGCAGAGAACGACGACGACGACGATGATGAAGAGACCATCCTATGTCTGCATCGA

Reverse complement sequence

TCGATGCAGACATAGGATGGTCTCTTCATCATCGTCGTCGTCGTCGTTCTCTGCCTGGACCACCTCTTCATCCTCCTCCGTCTCAGCAGGCAACGGGAAG[C/T]
GGCAGAGCGGGCAATGGCGGTTAATCAGAAGCCAGCTGAATATGCACTGCTCATGGAAGCAGTGCGAATCAGCGCACGGCATCTTCCTAAGCTTGTCGCC

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 54.70% 45.00% 0.04% 0.32% NA
All Indica  2759 29.70% 69.80% 0.07% 0.43% NA
All Japonica  1512 97.60% 2.40% 0.00% 0.00% NA
Aus  269 65.40% 33.50% 0.00% 1.12% NA
Indica I  595 81.50% 18.00% 0.00% 0.50% NA
Indica II  465 8.00% 91.60% 0.22% 0.22% NA
Indica III  913 8.80% 91.20% 0.00% 0.00% NA
Indica Intermediate  786 27.60% 71.20% 0.13% 1.02% NA
Temperate Japonica  767 97.40% 2.60% 0.00% 0.00% NA
Tropical Japonica  504 97.80% 2.20% 0.00% 0.00% NA
Japonica Intermediate  241 97.50% 2.50% 0.00% 0.00% NA
VI/Aromatic  96 54.20% 45.80% 0.00% 0.00% NA
Intermediate  90 68.90% 31.10% 0.00% 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
vg1101999349 G -> A LOC_Os11g04690.1 missense_variant ; p.Arg187His; MODERATE nonsynonymous_codon ; R187H Average:65.203; most accessible tissue: Minghui63 root, score: 76.721 benign 0.857 DELETERIOUS 0.00
vg1101999349 G -> DEL LOC_Os11g04690.1 N frameshift_variant Average:65.203; most accessible tissue: Minghui63 root, score: 76.721 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1101999349 NA 2.54E-10 mr1565 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
vg1101999349 NA 4.54E-10 mr1663 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
vg1101999349 NA 4.14E-07 mr1686 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
vg1101999349 NA 1.14E-06 mr1835 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
vg1101999349 2.15E-06 NA mr1904 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
vg1101999349 3.73E-08 3.94E-14 mr1904 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
vg1101999349 NA 4.39E-10 mr1024_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
vg1101999349 NA 1.23E-08 mr1078_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
vg1101999349 NA 2.93E-08 mr1265_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
vg1101999349 NA 2.73E-06 mr1486_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
vg1101999349 NA 5.96E-08 mr1528_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
vg1101999349 NA 1.08E-07 mr1558_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
vg1101999349 NA 1.25E-12 mr1565_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
vg1101999349 NA 1.07E-10 mr1565_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
vg1101999349 NA 7.43E-08 mr1593_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
vg1101999349 NA 2.46E-10 mr1659_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
vg1101999349 NA 2.00E-06 mr1659_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
vg1101999349 NA 1.55E-07 mr1683_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
vg1101999349 NA 1.22E-16 mr1715_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
vg1101999349 NA 1.07E-06 mr1735_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
vg1101999349 NA 2.72E-07 mr1824_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
vg1101999349 NA 2.74E-09 mr1835_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
vg1101999349 NA 1.48E-16 mr1838_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
vg1101999349 NA 1.86E-07 mr1838_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
vg1101999349 NA 3.48E-09 mr1904_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