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Detailed information for vg0121871143:

Variant ID: vg0121871143 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 21871143
Reference Allele: GAlternative Allele: C
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 227. )

Flanking Sequence (100 bp) in Reference Genome:


CCGAGAGATTCCTTCTCATTCTATCGGAAAGAGAGGATGTCTAATCAAAGATTAATTACACGGGTTAATGGAAAGAAAGCAAGGCAGAATTTGCACTTGA[G/C]
CTCCTCCCATTCACCGTGGAATTTCTTGACAGACATAGTGTACCATTGCTTCGCTCCATCTCTAAGAGAAAAAGGAAACAACTTCCACTTTATAGTTTCA

Reverse complement sequence

TGAAACTATAAAGTGGAAGTTGTTTCCTTTTTCTCTTAGAGATGGAGCGAAGCAATGGTACACTATGTCTGTCAAGAAATTCCACGGTGAATGGGAGGAG[C/G]
TCAAGTGCAAATTCTGCCTTGCTTTCTTTCCATTAACCCGTGTAATTAATCTTTGATTAGACATCCTCTCTTTCCGATAGAATGAGAAGGAATCTCTCGG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 56.10% 8.50% 6.22% 29.24% NA
All Indica  2759 28.90% 14.20% 9.89% 47.05% NA
All Japonica  1512 99.60% 0.00% 0.00% 0.40% NA
Aus  269 71.00% 1.10% 6.32% 21.56% NA
Indica I  595 8.60% 5.90% 11.26% 74.29% NA
Indica II  465 30.10% 17.40% 10.54% 41.94% NA
Indica III  913 31.40% 19.50% 10.19% 38.88% NA
Indica Intermediate  786 40.60% 12.30% 8.14% 38.93% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.40% 0.00% 0.00% 0.60% NA
Japonica Intermediate  241 98.80% 0.00% 0.00% 1.24% NA
VI/Aromatic  96 90.60% 3.10% 1.04% 5.21% NA
Intermediate  90 76.70% 3.30% 3.33% 16.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0121871143 G -> DEL N N silent_mutation Average:14.209; most accessible tissue: Minghui63 panicle, score: 20.733 N N N N
vg0121871143 G -> C LOC_Os01g38940.1 upstream_gene_variant ; 4982.0bp to feature; MODIFIER silent_mutation Average:14.209; most accessible tissue: Minghui63 panicle, score: 20.733 N N N N
vg0121871143 G -> C LOC_Os01g38930.1 intron_variant ; MODIFIER silent_mutation Average:14.209; most accessible tissue: Minghui63 panicle, score: 20.733 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0121871143 NA 1.65E-08 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
vg0121871143 NA 6.67E-06 mr1053 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
vg0121871143 NA 5.32E-07 mr1709 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
vg0121871143 NA 5.05E-08 mr1027_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
vg0121871143 NA 3.02E-08 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
vg0121871143 NA 3.24E-06 mr1045_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
vg0121871143 NA 1.17E-08 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
vg0121871143 NA 2.75E-07 mr1053_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
vg0121871143 NA 1.43E-06 mr1147_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
vg0121871143 NA 8.83E-06 mr1204_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
vg0121871143 2.13E-06 1.12E-07 mr1204_2 Ind_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
vg0121871143 2.87E-06 6.52E-09 mr1250_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
vg0121871143 9.86E-08 9.86E-08 mr1250_2 Ind_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
vg0121871143 NA 3.08E-06 mr1252_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
vg0121871143 NA 8.64E-06 mr1283_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
vg0121871143 NA 3.95E-06 mr1283_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
vg0121871143 7.90E-06 7.90E-06 mr1372_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
vg0121871143 2.22E-06 2.22E-06 mr1433_2 Ind_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
vg0121871143 4.26E-06 4.26E-06 mr1516_2 Ind_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
vg0121871143 7.98E-06 7.98E-06 mr1573_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
vg0121871143 NA 2.42E-06 mr1714_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
vg0121871143 NA 3.11E-06 mr1721_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
vg0121871143 NA 9.29E-06 mr1740_2 Ind_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
vg0121871143 NA 8.76E-06 mr1743_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
vg0121871143 NA 4.52E-06 mr1813_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
vg0121871143 9.02E-06 9.02E-06 mr1869_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
vg0121871143 NA 1.23E-06 mr1887_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
vg0121871143 NA 5.89E-08 mr1896_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