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Detailed information for vg0513460624:

Variant ID: vg0513460624 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 13460624
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GTATTATTCGGAATAAATCAAAAGCATAGAGATAAGATAAATTTATTTTCTGCTCTTACAATTGCAAAAGTACCCGAGTAGTAAATTTTGATTCGTGAAA[C/T]
TTTGTTCCATTAATGACGAACTCATGTCACTCATATGCATGTTTGGGAAGTGCCTAAACCAACTCCCGATGCTTGGGGGCTATGACTAGTCGGGCAGAGT

Reverse complement sequence

ACTCTGCCCGACTAGTCATAGCCCCCAAGCATCGGGAGTTGGTTTAGGCACTTCCCAAACATGCATATGAGTGACATGAGTTCGTCATTAATGGAACAAA[G/A]
TTTCACGAATCAAAATTTACTACTCGGGTACTTTTGCAATTGTAAGAGCAGAAAATAAATTTATCTTATCTCTATGCTTTTGATTTATTCCGAATAATAC

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 93.30% 2.40% 4.36% 0.00% NA
All Indica  2759 95.70% 0.30% 3.95% 0.00% NA
All Japonica  1512 87.60% 6.70% 5.69% 0.00% NA
Aus  269 97.80% 0.00% 2.23% 0.00% NA
Indica I  595 91.60% 0.70% 7.73% 0.00% NA
Indica II  465 95.30% 0.00% 4.73% 0.00% NA
Indica III  913 98.90% 0.10% 0.99% 0.00% NA
Indica Intermediate  786 95.40% 0.50% 4.07% 0.00% NA
Temperate Japonica  767 82.90% 9.90% 7.17% 0.00% NA
Tropical Japonica  504 96.00% 1.20% 2.78% 0.00% NA
Japonica Intermediate  241 85.10% 7.90% 7.05% 0.00% NA
VI/Aromatic  96 96.90% 1.00% 2.08% 0.00% NA
Intermediate  90 95.60% 1.10% 3.33% 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
vg0513460624 C -> T LOC_Os05g23500-LOC_Os05g23520 intergenic_region ; MODIFIER silent_mutation Average:38.945; most accessible tissue: Minghui63 flag leaf, score: 71.577 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0513460624 NA 8.50E-07 mr1028 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
vg0513460624 NA 6.02E-06 mr1028 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
vg0513460624 2.42E-06 NA mr1648 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
vg0513460624 NA 5.05E-08 mr1648 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
vg0513460624 2.72E-06 1.20E-07 mr1697 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
vg0513460624 3.40E-06 1.56E-09 mr1697 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