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Detailed information for vg1216757160:

Variant ID: vg1216757160 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 16757160
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTCGGACCATTGTTATTGAAGAACATGGCTTGGACGAGTGGTGTAGCGGCGTTGGCGACTTTCATCTCTACCTCCCTCAAGCCTCTTAATTTTGTTGACC[A/G]
AGACATCGAATTGAGCCTGAGATTTGATCTTGCGATCTACATAAATAGATTTATATCAACGAGTGGGCATAAAGAAAAGAATGGTTTTTAAAGTATTAGT

Reverse complement sequence

ACTAATACTTTAAAAACCATTCTTTTCTTTATGCCCACTCGTTGATATAAATCTATTTATGTAGATCGCAAGATCAAATCTCAGGCTCAATTCGATGTCT[T/C]
GGTCAACAAAATTAAGAGGCTTGAGGGAGGTAGAGATGAAAGTCGCCAACGCCGCTACACCACTCGTCCAAGCCATGTTCTTCAATAACAATGGTCCGAG

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 55.90% 15.70% 5.73% 22.64% NA
All Indica  2759 35.30% 19.00% 8.48% 37.22% NA
All Japonica  1512 94.20% 3.20% 1.52% 1.06% NA
Aus  269 33.80% 56.50% 2.60% 7.06% NA
Indica I  595 48.90% 27.10% 5.88% 18.15% NA
Indica II  465 50.80% 5.60% 8.17% 35.48% NA
Indica III  913 14.50% 19.90% 10.08% 55.53% NA
Indica Intermediate  786 39.90% 19.80% 8.78% 31.42% NA
Temperate Japonica  767 97.30% 1.70% 0.65% 0.39% NA
Tropical Japonica  504 90.30% 5.00% 2.78% 1.98% NA
Japonica Intermediate  241 92.50% 4.60% 1.66% 1.24% NA
VI/Aromatic  96 90.60% 7.30% 1.04% 1.04% NA
Intermediate  90 73.30% 12.20% 6.67% 7.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1216757160 A -> DEL N N silent_mutation Average:6.308; most accessible tissue: Zhenshan97 young leaf, score: 16.166 N N N N
vg1216757160 A -> G LOC_Os12g28330.1 downstream_gene_variant ; 765.0bp to feature; MODIFIER silent_mutation Average:6.308; most accessible tissue: Zhenshan97 young leaf, score: 16.166 N N N N
vg1216757160 A -> G LOC_Os12g28340.1 intron_variant ; MODIFIER silent_mutation Average:6.308; most accessible tissue: Zhenshan97 young leaf, score: 16.166 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1216757160 NA 7.61E-06 mr1864 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
vg1216757160 3.09E-06 3.08E-06 mr1207_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