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Detailed information for vg0704462910:

Variant ID: vg0704462910 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 4462910
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATGTTACCTGGATACAGCACAAAAGTGGCGTATCAGTATCGGATACGTGTATGGATATGGATACATATTGGATACACTTCGATACGTATCCCAGATTTTC[G/A]
CGATTTTCAGTTAAATAAAAAAAAGATACCTCGCCGATACGTCCCAAGCGTTCCTGAAAGGGTTAATTGGATACGTGCCATTAAAAATTTGCCAGTTTAG

Reverse complement sequence

CTAAACTGGCAAATTTTTAATGGCACGTATCCAATTAACCCTTTCAGGAACGCTTGGGACGTATCGGCGAGGTATCTTTTTTTTATTTAACTGAAAATCG[C/T]
GAAAATCTGGGATACGTATCGAAGTGTATCCAATATGTATCCATATCCATACACGTATCCGATACTGATACGCCACTTTTGTGCTGTATCCAGGTAACAT

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 79.60% 17.50% 2.94% 0.00% NA
All Indica  2759 99.20% 0.60% 0.22% 0.00% NA
All Japonica  1512 41.00% 50.40% 8.60% 0.00% NA
Aus  269 93.30% 6.70% 0.00% 0.00% NA
Indica I  595 98.80% 0.70% 0.50% 0.00% NA
Indica II  465 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 99.30% 0.40% 0.22% 0.00% NA
Indica Intermediate  786 99.00% 0.90% 0.13% 0.00% NA
Temperate Japonica  767 40.00% 46.80% 13.17% 0.00% NA
Tropical Japonica  504 44.00% 54.00% 1.98% 0.00% NA
Japonica Intermediate  241 37.80% 54.40% 7.88% 0.00% NA
VI/Aromatic  96 88.50% 10.40% 1.04% 0.00% NA
Intermediate  90 77.80% 20.00% 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
vg0704462910 G -> A LOC_Os07g08660.1 upstream_gene_variant ; 280.0bp to feature; MODIFIER silent_mutation Average:86.689; most accessible tissue: Zhenshan97 panicle, score: 93.558 N N N N
vg0704462910 G -> A LOC_Os07g08669.1 upstream_gene_variant ; 4431.0bp to feature; MODIFIER silent_mutation Average:86.689; most accessible tissue: Zhenshan97 panicle, score: 93.558 N N N N
vg0704462910 G -> A LOC_Os07g08650.1 downstream_gene_variant ; 3685.0bp to feature; MODIFIER silent_mutation Average:86.689; most accessible tissue: Zhenshan97 panicle, score: 93.558 N N N N
vg0704462910 G -> A LOC_Os07g08660-LOC_Os07g08669 intergenic_region ; MODIFIER silent_mutation Average:86.689; most accessible tissue: Zhenshan97 panicle, score: 93.558 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0704462910 2.81E-06 NA mr1008_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
vg0704462910 NA 2.23E-06 mr1020_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
vg0704462910 NA 1.95E-08 mr1660_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
vg0704462910 NA 1.63E-11 mr1714_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