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Detailed information for vg0106807279:

Variant ID: vg0106807279 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 6807279
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CCTCCGTCCAAAAAAAGACAAACCCTAGGTTTCCATGCTCAACGTTTGACTGTTCGTCTTATATGAAATTTTTTTATAATTAGTATTTTTATTGTTGTTA[G/T]
ATGATAAAACATGATTAATATTTTATGTGTGACTTATCTTTTTAATTTATTTTTATAATTTTTTTAAATAAAACGGGTGGTCAAATGTTGGACATGGAAA

Reverse complement sequence

TTTCCATGTCCAACATTTGACCACCCGTTTTATTTAAAAAAATTATAAAAATAAATTAAAAAGATAAGTCACACATAAAATATTAATCATGTTTTATCAT[C/A]
TAACAACAATAAAAATACTAATTATAAAAAAATTTCATATAAGACGAACAGTCAAACGTTGAGCATGGAAACCTAGGGTTTGTCTTTTTTTGGACGGAGG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 86.00% 13.70% 0.32% 0.00% NA
All Indica  2759 99.80% 0.20% 0.00% 0.00% NA
All Japonica  1512 59.10% 40.10% 0.79% 0.00% NA
Aus  269 98.50% 0.70% 0.74% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.40% 0.60% 0.00% 0.00% NA
Temperate Japonica  767 41.60% 57.10% 1.30% 0.00% NA
Tropical Japonica  504 86.70% 13.30% 0.00% 0.00% NA
Japonica Intermediate  241 57.30% 41.90% 0.83% 0.00% NA
VI/Aromatic  96 74.00% 26.00% 0.00% 0.00% NA
Intermediate  90 90.00% 8.90% 1.11% 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
vg0106807279 G -> T LOC_Os01g12430-LOC_Os01g12440 intergenic_region ; MODIFIER silent_mutation Average:70.672; most accessible tissue: Callus, score: 94.1 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0106807279 NA 5.27E-08 mr1624 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
vg0106807279 4.84E-06 4.84E-06 mr1050_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
vg0106807279 NA 4.75E-07 mr1549_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
vg0106807279 NA 1.20E-10 mr1624_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
vg0106807279 NA 1.03E-23 mr1679_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
vg0106807279 NA 2.39E-07 mr1679_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
vg0106807279 NA 2.23E-07 mr1733_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
vg0106807279 NA 2.05E-07 mr1757_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
vg0106807279 NA 8.81E-07 mr1780_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