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Detailed information for vg0712641791:

Variant ID: vg0712641791 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 12641791
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGCAAGATGTGCCTGTCTGCTTTGAAGACATGGAGGCGATCTTGGATTTCCACGTCTTTGAAATTCAAGATTTCGACATTCTAATCGGGCTTCCCATTGA[G/A]
CAACTTCTTATTAACACACCCCGATTAGGTAGCCTCAAAATAACACTGGGAGAGAATGAATTTTCAATTCCATTCTCGCGGGCAAGGATCACCTTGACCG

Reverse complement sequence

CGGTCAAGGTGATCCTTGCCCGCGAGAATGGAATTGAAAATTCATTCTCTCCCAGTGTTATTTTGAGGCTACCTAATCGGGGTGTGTTAATAAGAAGTTG[C/T]
TCAATGGGAAGCCCGATTAGAATGTCGAAATCTTGAATTTCAAAGACGTGGAAATCCAAGATCGCCTCCATGTCTTCAAAGCAGACAGGCACATCTTGCA

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 87.30% 4.70% 0.74% 7.19% NA
All Indica  2759 91.50% 0.10% 1.09% 7.36% NA
All Japonica  1512 87.10% 12.00% 0.13% 0.79% NA
Aus  269 44.20% 14.10% 0.74% 40.89% NA
Indica I  595 91.40% 0.00% 1.85% 6.72% NA
Indica II  465 89.70% 0.00% 1.08% 9.25% NA
Indica III  913 92.10% 0.00% 0.88% 7.01% NA
Indica Intermediate  786 91.90% 0.30% 0.76% 7.12% NA
Temperate Japonica  767 80.10% 19.00% 0.26% 0.65% NA
Tropical Japonica  504 99.60% 0.20% 0.00% 0.20% NA
Japonica Intermediate  241 83.40% 14.10% 0.00% 2.49% NA
VI/Aromatic  96 90.60% 2.10% 0.00% 7.29% NA
Intermediate  90 88.90% 1.10% 1.11% 8.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0712641791 G -> DEL LOC_Os07g22480.1 N frameshift_variant Average:13.86; most accessible tissue: Callus, score: 35.361 N N N N
vg0712641791 G -> A LOC_Os07g22480.1 synonymous_variant ; p.Glu115Glu; LOW synonymous_codon Average:13.86; most accessible tissue: Callus, score: 35.361 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0712641791 NA 1.88E-19 Awn_length All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0712641791 NA 1.54E-09 Awn_length Jap_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0712641791 NA 6.37E-06 mr1006 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
vg0712641791 NA 5.64E-06 mr1052 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
vg0712641791 4.89E-08 NA mr1549 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
vg0712641791 NA 1.09E-09 mr1549 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
vg0712641791 NA 1.02E-11 mr1624 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
vg0712641791 NA 8.28E-10 mr1624 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
vg0712641791 NA 4.65E-07 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
vg0712641791 NA 2.43E-07 mr1624_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