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Detailed information for vg0628893075:

Variant ID: vg0628893075 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 28893075
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTAGTGAAAGTTTGATCCGGCGTGGACAAAATAGCAGAAAGGCTTCAGCGACGTCACTCGCTGTCACTTCGGCTTGTCTACATTTATAGCAAGTGGTTAA[G/A]
GAGTTTTTTATCCTGGCATATGGGTCGCGACCTAGTCTTCGGGTTGTAGGGCCTTGATGTTGCACGCTGGTATTTTTTTCTCTTTTTTTAGTGTGTTGGA

Reverse complement sequence

TCCAACACACTAAAAAAAGAGAAAAAAATACCAGCGTGCAACATCAAGGCCCTACAACCCGAAGACTAGGTCGCGACCCATATGCCAGGATAAAAAACTC[C/T]
TTAACCACTTGCTATAAATGTAGACAAGCCGAAGTGACAGCGAGTGACGTCGCTGAAGCCTTTCTGCTATTTTGTCCACGCCGGATCAAACTTTCACTAA

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 85.60% 14.40% 0.00% 0.00% NA
All Indica  2759 88.80% 11.20% 0.00% 0.00% NA
All Japonica  1512 97.40% 2.60% 0.00% 0.00% NA
Aus  269 11.90% 88.10% 0.00% 0.00% NA
Indica I  595 87.70% 12.30% 0.00% 0.00% NA
Indica II  465 97.20% 2.80% 0.00% 0.00% NA
Indica III  913 88.40% 11.60% 0.00% 0.00% NA
Indica Intermediate  786 85.00% 15.00% 0.00% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 93.70% 6.30% 0.00% 0.00% NA
Japonica Intermediate  241 97.10% 2.90% 0.00% 0.00% NA
VI/Aromatic  96 10.40% 89.60% 0.00% 0.00% NA
Intermediate  90 92.20% 7.80% 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
vg0628893075 G -> A LOC_Os06g47740.1 upstream_gene_variant ; 925.0bp to feature; MODIFIER silent_mutation Average:56.008; most accessible tissue: Minghui63 root, score: 86.877 N N N N
vg0628893075 G -> A LOC_Os06g47740-LOC_Os06g47750 intergenic_region ; MODIFIER silent_mutation Average:56.008; most accessible tissue: Minghui63 root, score: 86.877 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0628893075 NA 3.00E-13 mr1166 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
vg0628893075 NA 5.85E-13 mr1231 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
vg0628893075 NA 8.73E-06 mr1305 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
vg0628893075 NA 9.28E-20 mr1515 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
vg0628893075 NA 6.15E-09 mr1515 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
vg0628893075 NA 6.44E-09 mr1585 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
vg0628893075 NA 3.88E-06 mr1633 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
vg0628893075 NA 3.92E-08 mr1669 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
vg0628893075 NA 2.39E-18 mr1765 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
vg0628893075 NA 4.80E-07 mr1923 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
vg0628893075 NA 9.01E-09 mr1166_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