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Detailed information for vg0912155913:

Variant ID: vg0912155913 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 12155913
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AGTGCCTCCGTAGTGCGCAGATTTTGACGCCGGCCCTTCGAGGGGCGAAGGTGGTTGGCTACTGGCGATGGCAGCTTCATGTATAGTGGGCTCTGGGCTT[C/T]
GGGCTCGCCTCGGGAGCTACAGGGACGACGGCATCGGGGGAGCGGCAGATCAGCCGCCGCCGGAGCTATGGTTCGGAACTAAGGATTCATGATTTTAGAA

Reverse complement sequence

TTCTAAAATCATGAATCCTTAGTTCCGAACCATAGCTCCGGCGGCGGCTGATCTGCCGCTCCCCCGATGCCGTCGTCCCTGTAGCTCCCGAGGCGAGCCC[G/A]
AAGCCCAGAGCCCACTATACATGAAGCTGCCATCGCCAGTAGCCAACCACCTTCGCCCCTCGAAGGGCCGGCGTCAAAATCTGCGCACTACGGAGGCACT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 98.40% 1.50% 0.06% 0.00% NA
All Indica  2759 99.80% 0.20% 0.00% 0.00% NA
All Japonica  1512 98.50% 1.30% 0.20% 0.00% NA
Aus  269 85.50% 14.50% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.20% 0.80% 0.00% 0.00% NA
Temperate Japonica  767 97.10% 2.50% 0.39% 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 93.80% 6.20% 0.00% 0.00% NA
Intermediate  90 96.70% 3.30% 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
vg0912155913 C -> T LOC_Os09g20270.1 upstream_gene_variant ; 1292.0bp to feature; MODIFIER silent_mutation Average:67.266; most accessible tissue: Zhenshan97 young leaf, score: 81.353 N N N N
vg0912155913 C -> T LOC_Os09g20260-LOC_Os09g20270 intergenic_region ; MODIFIER silent_mutation Average:67.266; most accessible tissue: Zhenshan97 young leaf, score: 81.353 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0912155913 NA 4.19E-08 mr1913 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
vg0912155913 NA 4.77E-06 mr1613_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
vg0912155913 4.54E-07 1.67E-08 mr1913_2 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