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Detailed information for vg1104181171:

Variant ID: vg1104181171 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 4181171
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGCATCGGTCTCACATTCGGAAAGCGCGAGAGCGAAGTGGTCTCGCACTTTTAGCGTGGGCCGGCCGGCCGACGCCGCCTGACGCACTCGGGCCAGGAAG[C/T]
GGTCTCGCACTTTGAGTGCGCAATAGCGTGTGCAGTATCGCGGTCGGCTCGCGTGAGACCGTAGCGACGGGGGCCGTCTGACGCACGTGGGTCCCGGAGA

Reverse complement sequence

TCTCCGGGACCCACGTGCGTCAGACGGCCCCCGTCGCTACGGTCTCACGCGAGCCGACCGCGATACTGCACACGCTATTGCGCACTCAAAGTGCGAGACC[G/A]
CTTCCTGGCCCGAGTGCGTCAGGCGGCGTCGGCCGGCCGGCCCACGCTAAAAGTGCGAGACCACTTCGCTCTCGCGCTTTCCGAATGTGAGACCGATGCA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 33.20% 7.30% 2.16% 57.36% NA
All Indica  2759 13.60% 0.40% 3.08% 82.93% NA
All Japonica  1512 66.10% 21.40% 0.26% 12.17% NA
Aus  269 58.70% 0.40% 3.35% 37.55% NA
Indica I  595 23.00% 0.00% 2.35% 74.62% NA
Indica II  465 10.10% 0.20% 3.66% 86.02% NA
Indica III  913 9.50% 0.20% 2.30% 87.95% NA
Indica Intermediate  786 13.20% 1.00% 4.20% 81.55% NA
Temperate Japonica  767 96.60% 2.30% 0.00% 1.04% NA
Tropical Japonica  504 15.70% 53.20% 0.79% 30.36% NA
Japonica Intermediate  241 74.70% 15.80% 0.00% 9.54% NA
VI/Aromatic  96 8.30% 0.00% 1.04% 90.62% NA
Intermediate  90 30.00% 10.00% 3.33% 56.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1104181171 C -> T LOC_Os11g08040.1 downstream_gene_variant ; 1438.0bp to feature; MODIFIER silent_mutation Average:8.873; most accessible tissue: Callus, score: 32.206 N N N N
vg1104181171 C -> T LOC_Os11g08050.1 downstream_gene_variant ; 3021.0bp to feature; MODIFIER silent_mutation Average:8.873; most accessible tissue: Callus, score: 32.206 N N N N
vg1104181171 C -> T LOC_Os11g08020-LOC_Os11g08040 intergenic_region ; MODIFIER silent_mutation Average:8.873; most accessible tissue: Callus, score: 32.206 N N N N
vg1104181171 C -> DEL N N silent_mutation Average:8.873; most accessible tissue: Callus, score: 32.206 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1104181171 NA 1.74E-06 mr1179 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
vg1104181171 NA 2.64E-06 mr1248 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
vg1104181171 NA 6.05E-07 mr1338 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
vg1104181171 NA 3.43E-06 mr1518 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
vg1104181171 6.61E-08 5.73E-12 mr1539 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
vg1104181171 NA 2.20E-06 mr1826 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
vg1104181171 7.97E-08 NA mr1136_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
vg1104181171 NA 1.21E-07 mr1408_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
vg1104181171 NA 5.05E-09 mr1676_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
vg1104181171 NA 4.33E-07 mr1696_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