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Detailed information for vg1014485975:

Variant ID: vg1014485975 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 14485975
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AGAAACTAAAAAGGAAAAGATAAAGTTCTTATCGGACACTAAACACACTTTCCTAAAGATAAAAGAAAACTAACAAACTACGCCTAATTAATAGATAACT[G/A]
TCATGTCGTATCCTTCTTGAACTCGAACTCCGACGAGATCGAGCGGGGGGTCGGTGGTCTACGGGCTACAGCTTCGGATCCATCTGCATCGCCGGGATCA

Reverse complement sequence

TGATCCCGGCGATGCAGATGGATCCGAAGCTGTAGCCCGTAGACCACCGACCCCCCGCTCGATCTCGTCGGAGTTCGAGTTCAAGAAGGATACGACATGA[C/T]
AGTTATCTATTAATTAGGCGTAGTTTGTTAGTTTTCTTTTATCTTTAGGAAAGTGTGTTTAGTGTCCGATAAGAACTTTATCTTTTCCTTTTTAGTTTCT

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 96.60% 2.40% 0.47% 0.51% NA
All Indica  2759 95.00% 4.10% 0.80% 0.11% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 92.90% 0.00% 0.00% 7.06% NA
Indica I  595 81.30% 15.30% 3.36% 0.00% NA
Indica II  465 99.60% 0.20% 0.22% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 96.90% 2.50% 0.13% 0.38% 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  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 95.60% 2.20% 0.00% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1014485975 G -> A LOC_Os10g27470.1 upstream_gene_variant ; 1158.0bp to feature; MODIFIER silent_mutation Average:74.227; most accessible tissue: Minghui63 panicle, score: 82.128 N N N N
vg1014485975 G -> A LOC_Os10g27460.1 downstream_gene_variant ; 98.0bp to feature; MODIFIER silent_mutation Average:74.227; most accessible tissue: Minghui63 panicle, score: 82.128 N N N N
vg1014485975 G -> A LOC_Os10g27450-LOC_Os10g27460 intergenic_region ; MODIFIER silent_mutation Average:74.227; most accessible tissue: Minghui63 panicle, score: 82.128 N N N N
vg1014485975 G -> DEL N N silent_mutation Average:74.227; most accessible tissue: Minghui63 panicle, score: 82.128 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1014485975 2.51E-06 9.11E-12 mr1038 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
vg1014485975 5.98E-09 8.90E-09 mr1141 Ind_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
vg1014485975 4.50E-08 7.59E-15 mr1389 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
vg1014485975 3.53E-08 3.50E-14 mr1038_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
vg1014485975 4.55E-06 3.33E-12 mr1389_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