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Detailed information for vg1200761684:

Variant ID: vg1200761684 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 761684
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CATTAAATCTATAATTGAATAATTTTTCATAATATACTTGTCTTGGGTTAAAAATGTTACTACTTTTTTTCTACAAAATCAGTCAAACTTATAATAGTTC[G/A]
ACTTTGACTAAAGTCAAAACGTCTTATAACCTGAAACGGAGTAATAGTTAATAAAAACTTTTACAAGTTAAAATAGATTATCATATGTGAGATATATCTC

Reverse complement sequence

GAGATATATCTCACATATGATAATCTATTTTAACTTGTAAAAGTTTTTATTAACTATTACTCCGTTTCAGGTTATAAGACGTTTTGACTTTAGTCAAAGT[C/T]
GAACTATTATAAGTTTGACTGATTTTGTAGAAAAAAAGTAGTAACATTTTTAACCCAAGACAAGTATATTATGAAAAATTATTCAATTATAGATTTAATG

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 92.80% 7.10% 0.08% 0.00% NA
All Indica  2759 87.80% 12.00% 0.14% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.50% 0.50% 0.00% 0.00% NA
Indica II  465 98.50% 1.50% 0.00% 0.00% NA
Indica III  913 72.50% 27.10% 0.44% 0.00% NA
Indica Intermediate  786 90.50% 9.50% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 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
vg1200761684 G -> A LOC_Os12g02350.1 upstream_gene_variant ; 2107.0bp to feature; MODIFIER silent_mutation Average:32.763; most accessible tissue: Zhenshan97 flower, score: 75.657 N N N N
vg1200761684 G -> A LOC_Os12g02370.2 downstream_gene_variant ; 4750.0bp to feature; MODIFIER silent_mutation Average:32.763; most accessible tissue: Zhenshan97 flower, score: 75.657 N N N N
vg1200761684 G -> A LOC_Os12g02370.4 downstream_gene_variant ; 4750.0bp to feature; MODIFIER silent_mutation Average:32.763; most accessible tissue: Zhenshan97 flower, score: 75.657 N N N N
vg1200761684 G -> A LOC_Os12g02340.1 intron_variant ; MODIFIER silent_mutation Average:32.763; most accessible tissue: Zhenshan97 flower, score: 75.657 N N N N
vg1200761684 G -> A LOC_Os12g02340.2 intron_variant ; MODIFIER silent_mutation Average:32.763; most accessible tissue: Zhenshan97 flower, score: 75.657 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1200761684 NA 8.30E-07 mr1111 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
vg1200761684 NA 1.29E-07 mr1244 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