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Detailed information for vg0920292378:

Variant ID: vg0920292378 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 20292378
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGGGCCCTTTTGGATCGCAGAATTAAAATTACGATTTTGCTATATCTCACTCGAAAGATTTTTTCTTATCTCTCACTCGATTTTCTTACTCAAATTTACA[A/G]
TGTATTTTCTTGTAAGTTACAGTGTAATTTATGAAACTTACACTGTAACTTTTGTAAGTTACACTGTAATTTTTAAATCTTCACATGTAAATTTTAAATT

Reverse complement sequence

AATTTAAAATTTACATGTGAAGATTTAAAAATTACAGTGTAACTTACAAAAGTTACAGTGTAAGTTTCATAAATTACACTGTAACTTACAAGAAAATACA[T/C]
TGTAAATTTGAGTAAGAAAATCGAGTGAGAGATAAGAAAAAATCTTTCGAGTGAGATATAGCAAAATCGTAATTTTAATTCTGCGATCCAAAAGGGCCCA

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 36.00% 1.10% 7.38% 55.52% NA
All Indica  2759 4.50% 0.80% 9.06% 85.65% NA
All Japonica  1512 96.50% 1.50% 1.65% 0.33% NA
Aus  269 1.90% 0.70% 15.61% 81.78% NA
Indica I  595 5.50% 0.30% 8.74% 85.38% NA
Indica II  465 6.50% 1.50% 9.25% 82.80% NA
Indica III  913 1.50% 1.00% 8.43% 89.05% NA
Indica Intermediate  786 5.90% 0.60% 9.92% 83.59% NA
Temperate Japonica  767 98.70% 1.30% 0.00% 0.00% NA
Tropical Japonica  504 95.00% 2.40% 2.18% 0.40% NA
Japonica Intermediate  241 92.50% 0.40% 5.81% 1.24% NA
VI/Aromatic  96 59.40% 6.20% 25.00% 9.38% NA
Intermediate  90 61.10% 0.00% 8.89% 30.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0920292378 A -> G LOC_Os09g34340-LOC_Os09g34847 intergenic_region ; MODIFIER silent_mutation Average:19.21; most accessible tissue: Minghui63 panicle, score: 25.313 N N N N
vg0920292378 A -> DEL N N silent_mutation Average:19.21; most accessible tissue: Minghui63 panicle, score: 25.313 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0920292378 4.46E-06 NA mr1062 Jap_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
vg0920292378 NA 4.17E-06 mr1216 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
vg0920292378 NA 5.04E-09 mr1410 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
vg0920292378 NA 3.51E-07 mr1510 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
vg0920292378 2.16E-07 9.32E-27 mr1518 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
vg0920292378 9.69E-09 1.04E-12 mr1518 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
vg0920292378 5.19E-07 4.28E-29 mr1676 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
vg0920292378 6.06E-09 4.09E-14 mr1676 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
vg0920292378 NA 6.95E-29 mr1676_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
vg0920292378 3.43E-10 2.00E-17 mr1676_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