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Detailed information for vg1201024139:

Variant ID: vg1201024139 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 1024139
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CCATAATAGGTGACATTTTTGACTTTTTATTTGCAACATTTGACCATTCGTTTTATTTGAAAAATTAGTGCAAATATTAAAAAAAAGATAAGTCATATGT[A/G]
AAGTAATTTTGATAATAAAGCAATTGACAAACAAAATAAATAATAATTTCAAAATTTTTTAAATAAGACGAATGATCAAACATTGACAAACAAAAAAAAC

Reverse complement sequence

GTTTTTTTTGTTTGTCAATGTTTGATCATTCGTCTTATTTAAAAAATTTTGAAATTATTATTTATTTTGTTTGTCAATTGCTTTATTATCAAAATTACTT[T/C]
ACATATGACTTATCTTTTTTTTAATATTTGCACTAATTTTTCAAATAAAACGAATGGTCAAATGTTGCAAATAAAAAGTCAAAAATGTCACCTATTATGG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 91.50% 8.50% 0.00% 0.00% NA
All Indica  2759 94.90% 5.10% 0.00% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 4.10% 95.90% 0.00% 0.00% NA
Indica I  595 98.20% 1.80% 0.00% 0.00% NA
Indica II  465 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 94.30% 5.70% 0.00% 0.00% NA
Indica Intermediate  786 90.30% 9.70% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 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
vg1201024139 A -> G LOC_Os12g02840.1 downstream_gene_variant ; 2963.0bp to feature; MODIFIER silent_mutation Average:51.253; most accessible tissue: Zhenshan97 panicle, score: 83.41 N N N N
vg1201024139 A -> G LOC_Os12g02840-LOC_Os12g02850 intergenic_region ; MODIFIER silent_mutation Average:51.253; most accessible tissue: Zhenshan97 panicle, score: 83.41 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1201024139 NA 3.16E-15 mr1158 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
vg1201024139 1.61E-07 NA mr1261 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
vg1201024139 NA 9.59E-06 mr1634 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
vg1201024139 NA 3.53E-11 mr1649 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
vg1201024139 NA 3.76E-10 mr1696 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
vg1201024139 NA 8.08E-24 mr1095_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
vg1201024139 NA 4.70E-29 mr1098_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
vg1201024139 NA 2.06E-24 mr1099_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
vg1201024139 NA 3.21E-12 mr1409_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
vg1201024139 NA 9.88E-16 mr1911_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