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Detailed information for vg1220827723:

Variant ID: vg1220827723 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 20827723
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATGTTGAGAAACATACAGTGGTCTTTCGGCTAGCTCCACAAGGTAATGGGCTAGACGATTTGAGTTCAAAGTCTAATCATTTTTAATTATTTGATATTAG[G/A]
TCATTCCCTAATATTCACATCTTTTTAGGGATATGATAATGTGTATTAGGGATTAGTAAGCATGCGAGAAGAAAAAACTAATTTTATATATATATATATA

Reverse complement sequence

TATATATATATATATAAAATTAGTTTTTTCTTCTCGCATGCTTACTAATCCCTAATACACATTATCATATCCCTAAAAAGATGTGAATATTAGGGAATGA[C/T]
CTAATATCAAATAATTAAAAATGATTAGACTTTGAACTCAAATCGTCTAGCCCATTACCTTGTGGAGCTAGCCGAAAGACCACTGTATGTTTCTCAACAT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 91.00% 7.40% 0.32% 1.31% NA
All Indica  2759 98.60% 0.30% 0.22% 0.91% NA
All Japonica  1512 80.10% 19.80% 0.07% 0.00% NA
Aus  269 72.90% 11.50% 2.97% 12.64% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 99.60% 0.00% 0.00% 0.43% NA
Indica III  913 98.00% 0.30% 0.44% 1.20% NA
Indica Intermediate  786 97.80% 0.40% 0.25% 1.53% NA
Temperate Japonica  767 81.00% 19.00% 0.00% 0.00% NA
Tropical Japonica  504 81.90% 18.10% 0.00% 0.00% NA
Japonica Intermediate  241 73.40% 26.10% 0.41% 0.00% NA
VI/Aromatic  96 93.80% 3.10% 0.00% 3.12% NA
Intermediate  90 92.20% 7.80% 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
vg1220827723 G -> DEL N N silent_mutation Average:50.702; most accessible tissue: Callus, score: 88.397 N N N N
vg1220827723 G -> A LOC_Os12g34360.1 upstream_gene_variant ; 1251.0bp to feature; MODIFIER silent_mutation Average:50.702; most accessible tissue: Callus, score: 88.397 N N N N
vg1220827723 G -> A LOC_Os12g34350-LOC_Os12g34360 intergenic_region ; MODIFIER silent_mutation Average:50.702; most accessible tissue: Callus, score: 88.397 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1220827723 NA 3.97E-07 mr1057 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
vg1220827723 NA 6.93E-06 mr1057 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
vg1220827723 4.48E-11 NA mr1334 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
vg1220827723 NA 4.04E-08 mr1057_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
vg1220827723 NA 8.32E-07 mr1057_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
vg1220827723 4.30E-12 NA mr1334_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
vg1220827723 7.73E-06 NA mr1991_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