\

Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0819180192:

Variant ID: vg0819180192 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 19180192
Reference Allele: TAlternative Allele: G
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TAAATTCTTAAAATATACTCCCTCCGTCCCCAAATATAAGGGATTTTGAACGGATGTGACATTTTTTAAGTGCTACGAATCAGGACAGGGAGCATGTTTA[T/G]
CAATCCCCTCCTATCTCACTTATATTTTAATATTTTAGGACGGAGGGAGTACTTCGTCTAGCAGGCAAATGTTTAGCAATCCCCTCCTATCTCTATTCTC

Reverse complement sequence

GAGAATAGAGATAGGAGGGGATTGCTAAACATTTGCCTGCTAGACGAAGTACTCCCTCCGTCCTAAAATATTAAAATATAAGTGAGATAGGAGGGGATTG[A/C]
TAAACATGCTCCCTGTCCTGATTCGTAGCACTTAAAAAATGTCACATCCGTTCAAAATCCCTTATATTTGGGGACGGAGGGAGTATATTTTAAGAATTTA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 86.50% 10.50% 2.96% 0.00% NA
All Indica  2759 98.80% 0.70% 0.47% 0.00% NA
All Japonica  1512 61.40% 30.80% 7.80% 0.00% NA
Aus  269 98.50% 1.50% 0.00% 0.00% NA
Indica I  595 97.30% 1.00% 1.68% 0.00% NA
Indica II  465 99.40% 0.60% 0.00% 0.00% NA
Indica III  913 99.60% 0.40% 0.00% 0.00% NA
Indica Intermediate  786 98.90% 0.80% 0.38% 0.00% NA
Temperate Japonica  767 35.20% 52.90% 11.86% 0.00% NA
Tropical Japonica  504 94.20% 3.80% 1.98% 0.00% NA
Japonica Intermediate  241 76.30% 16.60% 7.05% 0.00% NA
VI/Aromatic  96 95.80% 2.10% 2.08% 0.00% NA
Intermediate  90 83.30% 8.90% 7.78% 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
vg0819180192 T -> G LOC_Os08g31070.1 upstream_gene_variant ; 4178.0bp to feature; MODIFIER silent_mutation Average:33.88; most accessible tissue: Callus, score: 59.922 N N N N
vg0819180192 T -> G LOC_Os08g31060.1 intron_variant ; MODIFIER silent_mutation Average:33.88; most accessible tissue: Callus, score: 59.922 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0819180192 NA 2.48E-07 mr1002 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
vg0819180192 NA 1.85E-06 mr1002 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
vg0819180192 NA 1.61E-06 mr1183 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
vg0819180192 NA 1.64E-06 mr1503 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
vg0819180192 NA 2.50E-13 mr1002_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
vg0819180192 NA 1.09E-10 mr1002_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
vg0819180192 NA 1.31E-13 mr1182_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
vg0819180192 NA 7.42E-07 mr1182_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
vg0819180192 NA 3.64E-10 mr1282_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
vg0819180192 NA 1.13E-06 mr1330_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
vg0819180192 NA 7.09E-06 mr1371_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
vg0819180192 NA 5.55E-06 mr1648_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
vg0819180192 NA 2.24E-08 mr1794_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
vg0819180192 NA 4.21E-08 mr1805_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
vg0819180192 1.77E-06 NA mr1851_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
vg0819180192 NA 1.60E-06 mr1851_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
vg0819180192 NA 1.80E-06 mr1977_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