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Detailed information for vg0220960199:

Variant ID: vg0220960199 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 20960199
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATGATATTTATCGATTCACCAGAAATTAAGTTTAAATTTGACATGCACCTTGAAAAAAAAAGATAAATTCGGGTATGGACACTACCACTACCCTATTATT[C/T]
ATATACCGAATTTATGTTTTTTATATATCAATGTGTAAGTTGAGTTTGGATCTTACATTTTTTTAGAGGTGGTATATGTATTTGTACGAACGCTGTCAAC

Reverse complement sequence

GTTGACAGCGTTCGTACAAATACATATACCACCTCTAAAAAAATGTAAGATCCAAACTCAACTTACACATTGATATATAAAAAACATAAATTCGGTATAT[G/A]
AATAATAGGGTAGTGGTAGTGTCCATACCCGAATTTATCTTTTTTTTTCAAGGTGCATGTCAAATTTAAACTTAATTTCTGGTGAATCGATAAATATCAT

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 98.20% 1.80% 0.04% 0.00% NA
All Indica  2759 99.40% 0.60% 0.00% 0.00% NA
All Japonica  1512 95.60% 4.20% 0.13% 0.00% NA
Aus  269 99.30% 0.70% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.40% 0.60% 0.00% 0.00% NA
Indica III  913 99.10% 0.90% 0.00% 0.00% NA
Indica Intermediate  786 99.40% 0.60% 0.00% 0.00% NA
Temperate Japonica  767 95.00% 4.80% 0.13% 0.00% NA
Tropical Japonica  504 95.20% 4.60% 0.20% 0.00% NA
Japonica Intermediate  241 98.30% 1.70% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 97.80% 2.20% 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
vg0220960199 C -> T LOC_Os02g34930.1 downstream_gene_variant ; 3914.0bp to feature; MODIFIER silent_mutation Average:62.924; most accessible tissue: Callus, score: 84.176 N N N N
vg0220960199 C -> T LOC_Os02g34950.1 downstream_gene_variant ; 2739.0bp to feature; MODIFIER silent_mutation Average:62.924; most accessible tissue: Callus, score: 84.176 N N N N
vg0220960199 C -> T LOC_Os02g34940.1 intron_variant ; MODIFIER silent_mutation Average:62.924; most accessible tissue: Callus, score: 84.176 N N N N
vg0220960199 C -> T LOC_Os02g34940.2 intron_variant ; MODIFIER silent_mutation Average:62.924; most accessible tissue: Callus, score: 84.176 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0220960199 NA 6.22E-07 mr1069 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
vg0220960199 1.62E-06 1.62E-06 mr1098 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
vg0220960199 7.83E-09 7.83E-09 mr1099 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
vg0220960199 5.32E-09 8.98E-10 mr1101 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
vg0220960199 1.31E-06 7.81E-07 mr1123 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
vg0220960199 7.00E-08 4.83E-08 mr1150 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
vg0220960199 1.31E-06 2.01E-06 mr1242 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
vg0220960199 1.71E-06 4.68E-07 mr1247 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
vg0220960199 7.85E-06 7.85E-06 mr1589 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
vg0220960199 2.43E-06 2.43E-06 mr1595 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
vg0220960199 NA 6.84E-06 mr1858 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
vg0220960199 NA 6.84E-06 mr1859 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
vg0220960199 9.26E-06 9.27E-06 mr1868 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
vg0220960199 NA 8.52E-06 mr1917 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
vg0220960199 7.10E-07 8.95E-09 mr1098_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
vg0220960199 6.57E-06 6.24E-07 mr1099_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
vg0220960199 3.19E-06 8.55E-08 mr1150_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
vg0220960199 NA 6.01E-06 mr1240_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