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Detailed information for vg0605181590:

Variant ID: vg0605181590 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 5181590
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AAAAAATGTTACTCCCTCCGTTTTATAATGTAAGTCATTCTAGCATTTCCCACATTCATATTGATGTTAATGAATCTAGATAGATATATATGTCTAGATT[T/C]
ATTAACATTAATATGAATGTGGGAAATGCTAAAATGACTTATATTATGAAACGGAGGGAGTAGCCTTTAGGAAAATGAGCATGTGCATTGCTAGCAGTTT

Reverse complement sequence

AAACTGCTAGCAATGCACATGCTCATTTTCCTAAAGGCTACTCCCTCCGTTTCATAATATAAGTCATTTTAGCATTTCCCACATTCATATTAATGTTAAT[A/G]
AATCTAGACATATATATCTATCTAGATTCATTAACATCAATATGAATGTGGGAAATGCTAGAATGACTTACATTATAAAACGGAGGGAGTAACATTTTTT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 84.80% 14.60% 0.53% 0.00% NA
All Indica  2759 94.30% 5.70% 0.07% 0.00% NA
All Japonica  1512 68.40% 30.20% 1.39% 0.00% NA
Aus  269 77.30% 22.70% 0.00% 0.00% NA
Indica I  595 97.50% 2.50% 0.00% 0.00% NA
Indica II  465 98.50% 1.50% 0.00% 0.00% NA
Indica III  913 94.60% 5.40% 0.00% 0.00% NA
Indica Intermediate  786 88.90% 10.80% 0.25% 0.00% NA
Temperate Japonica  767 84.10% 13.70% 2.22% 0.00% NA
Tropical Japonica  504 44.00% 55.80% 0.20% 0.00% NA
Japonica Intermediate  241 69.30% 29.50% 1.24% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 78.90% 18.90% 2.22% 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
vg0605181590 T -> C LOC_Os06g10130.1 downstream_gene_variant ; 842.0bp to feature; MODIFIER silent_mutation Average:34.753; most accessible tissue: Minghui63 panicle, score: 70.194 N N N N
vg0605181590 T -> C LOC_Os06g10140.1 downstream_gene_variant ; 4857.0bp to feature; MODIFIER silent_mutation Average:34.753; most accessible tissue: Minghui63 panicle, score: 70.194 N N N N
vg0605181590 T -> C LOC_Os06g10130-LOC_Os06g10140 intergenic_region ; MODIFIER silent_mutation Average:34.753; most accessible tissue: Minghui63 panicle, score: 70.194 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0605181590 5.27E-06 1.16E-10 mr1201 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
vg0605181590 NA 3.03E-14 mr1201 Ind_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
vg0605181590 2.17E-06 2.05E-10 mr1219 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
vg0605181590 NA 1.94E-13 mr1219 Ind_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
vg0605181590 2.88E-07 1.55E-12 mr1274 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
vg0605181590 2.20E-06 8.34E-16 mr1274 Ind_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
vg0605181590 NA 5.24E-09 mr1805 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
vg0605181590 9.33E-06 1.59E-09 mr1201_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
vg0605181590 NA 4.36E-11 mr1201_2 Ind_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
vg0605181590 NA 1.85E-08 mr1219_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
vg0605181590 NA 4.28E-10 mr1219_2 Ind_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
vg0605181590 4.93E-06 5.29E-10 mr1274_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
vg0605181590 NA 1.70E-13 mr1274_2 Ind_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
vg0605181590 NA 1.88E-07 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