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Detailed information for vg1122485909:

Variant ID: vg1122485909 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 22485909
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GACCTGATGTCCAATAAAAAATAAATCCGAACGGATGGGAGTTAATTATAGGACAGCTCGTGTGATTTATCAATCATCAGTTGGGGTCGGGAATTGGGAT[A/T]
GCTGGTATCAATCTTCACTCCCCATTCTTTTCTCCAACAAAAGTTAGATAAACTTTTGGATACTCGTGACAAGCTTTTCAAACTGCTAGACGGTGTGTTT

Reverse complement sequence

AAACACACCGTCTAGCAGTTTGAAAAGCTTGTCACGAGTATCCAAAAGTTTATCTAACTTTTGTTGGAGAAAAGAATGGGGAGTGAAGATTGATACCAGC[T/A]
ATCCCAATTCCCGACCCCAACTGATGATTGATAAATCACACGAGCTGTCCTATAATTAACTCCCATCCGTTCGGATTTATTTTTTATTGGACATCAGGTC

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 80.80% 19.20% 0.04% 0.00% NA
All Indica  2759 92.60% 7.40% 0.04% 0.00% NA
All Japonica  1512 56.50% 43.50% 0.00% 0.00% NA
Aus  269 89.60% 10.00% 0.37% 0.00% NA
Indica I  595 99.70% 0.30% 0.00% 0.00% NA
Indica II  465 97.40% 2.60% 0.00% 0.00% NA
Indica III  913 82.80% 17.10% 0.11% 0.00% NA
Indica Intermediate  786 95.70% 4.30% 0.00% 0.00% NA
Temperate Japonica  767 51.90% 48.10% 0.00% 0.00% NA
Tropical Japonica  504 69.60% 30.40% 0.00% 0.00% NA
Japonica Intermediate  241 44.00% 56.00% 0.00% 0.00% NA
VI/Aromatic  96 91.70% 8.30% 0.00% 0.00% NA
Intermediate  90 87.80% 12.20% 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
vg1122485909 A -> T LOC_Os11g37910.1 upstream_gene_variant ; 3254.0bp to feature; MODIFIER silent_mutation Average:36.184; most accessible tissue: Minghui63 root, score: 41.911 N N N N
vg1122485909 A -> T LOC_Os11g37900-LOC_Os11g37910 intergenic_region ; MODIFIER silent_mutation Average:36.184; most accessible tissue: Minghui63 root, score: 41.911 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1122485909 2.77E-08 NA mr1238 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
vg1122485909 9.77E-07 NA mr1309 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
vg1122485909 6.51E-08 NA mr1238_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
vg1122485909 2.03E-08 NA mr1484_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
vg1122485909 9.03E-06 NA mr1609_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
vg1122485909 8.95E-09 NA mr1841_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
vg1122485909 2.74E-06 NA mr1841_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
vg1122485909 1.20E-06 NA mr1900_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
vg1122485909 7.23E-07 NA mr1945_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