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Detailed information for vg1122067670:

Variant ID: vg1122067670 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 22067670
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AAATTTATGCACCTAAAGTTTGTACACCTCAAGTTTATACATCTAAAGTTTAGAAACCTAAAGTTTATAAGTCAAAAGTTTATATATCCGATTCAAATTT[G/A]
AATTTAAATTCAAATTTTTTTTATATATAGTATTTCTATATATCTAAAGTTTATACACCTAAAGTTTATAGACCCAAAGTTTATAAGTCAAAAGTTTACA

Reverse complement sequence

TGTAAACTTTTGACTTATAAACTTTGGGTCTATAAACTTTAGGTGTATAAACTTTAGATATATAGAAATACTATATATAAAAAAAATTTGAATTTAAATT[C/T]
AAATTTGAATCGGATATATAAACTTTTGACTTATAAACTTTAGGTTTCTAAACTTTAGATGTATAAACTTGAGGTGTACAAACTTTAGGTGCATAAATTT

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 78.00% 16.50% 0.49% 5.01% NA
All Indica  2759 89.20% 6.40% 0.58% 3.84% NA
All Japonica  1512 62.60% 34.60% 0.40% 2.45% NA
Aus  269 71.00% 2.60% 0.37% 26.02% NA
Indica I  595 96.60% 2.40% 0.84% 0.17% NA
Indica II  465 99.10% 0.40% 0.00% 0.43% NA
Indica III  913 82.40% 10.10% 0.11% 7.45% NA
Indica Intermediate  786 85.50% 8.80% 1.27% 4.45% NA
Temperate Japonica  767 78.60% 20.20% 0.78% 0.39% NA
Tropical Japonica  504 45.60% 49.00% 0.00% 5.36% NA
Japonica Intermediate  241 46.90% 50.20% 0.00% 2.90% NA
VI/Aromatic  96 24.00% 57.30% 0.00% 18.75% NA
Intermediate  90 73.30% 20.00% 0.00% 6.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1122067670 G -> A LOC_Os11g37390.1 upstream_gene_variant ; 434.0bp to feature; MODIFIER silent_mutation Average:37.808; most accessible tissue: Minghui63 panicle, score: 59.629 N N N N
vg1122067670 G -> A LOC_Os11g37380-LOC_Os11g37390 intergenic_region ; MODIFIER silent_mutation Average:37.808; most accessible tissue: Minghui63 panicle, score: 59.629 N N N N
vg1122067670 G -> DEL N N silent_mutation Average:37.808; most accessible tissue: Minghui63 panicle, score: 59.629 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1122067670 NA 2.92E-13 mr1084 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
vg1122067670 NA 1.23E-06 mr1209 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
vg1122067670 NA 9.77E-07 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
vg1122067670 NA 2.08E-06 mr1229 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
vg1122067670 NA 8.34E-09 mr1278 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
vg1122067670 NA 7.42E-06 mr1293 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
vg1122067670 NA 3.69E-07 mr1418 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
vg1122067670 NA 1.36E-06 mr1420 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
vg1122067670 NA 1.56E-06 mr1461 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
vg1122067670 NA 3.69E-09 mr1506 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
vg1122067670 NA 3.43E-07 mr1508 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
vg1122067670 NA 2.39E-12 mr1521 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
vg1122067670 NA 5.39E-06 mr1596 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
vg1122067670 3.67E-06 NA mr1611 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
vg1122067670 NA 8.42E-07 mr1729 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
vg1122067670 NA 2.21E-11 mr1775 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
vg1122067670 NA 4.39E-09 mr1776 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
vg1122067670 NA 3.59E-07 mr1779 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
vg1122067670 NA 1.59E-06 mr1812 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
vg1122067670 6.83E-07 7.28E-11 mr1824 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
vg1122067670 NA 7.50E-06 mr1832 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
vg1122067670 NA 2.61E-06 mr1992 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