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Detailed information for vg0110837074:

Variant ID: vg0110837074 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 10837074
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GCTGGCCGACGGGGGCGTCGGTGCAGGGCCACATGTCGGCAGAGTTTGAGTGGTGGTGGAGCATCGGTGCATCAGCCGTAGATTCGCAGGTGGTGAGCGG[C/T]
GGGTGAAAACCTAGCTCGGCCTTGGCCGGACCGACAACGATGAATTCCCCCTCCTGAAGGCGTTGTCGTGCTGTCTCACCCCTCAAGGGTGATTGCCGGG

Reverse complement sequence

CCCGGCAATCACCCTTGAGGGGTGAGACAGCACGACAACGCCTTCAGGAGGGGGAATTCATCGTTGTCGGTCCGGCCAAGGCCGAGCTAGGTTTTCACCC[G/A]
CCGCTCACCACCTGCGAATCTACGGCTGATGCACCGATGCTCCACCACCACTCAAACTCTGCCGACATGTGGCCCTGCACCGACGCCCCCGTCGGCCAGC

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 94.00% 5.90% 0.06% 0.00% NA
All Indica  2759 94.70% 5.30% 0.00% 0.00% NA
All Japonica  1512 99.80% 0.20% 0.00% 0.00% NA
Aus  269 52.80% 46.80% 0.37% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 99.40% 0.60% 0.00% 0.00% NA
Indica III  913 90.70% 9.30% 0.00% 0.00% NA
Indica Intermediate  786 92.70% 7.30% 0.00% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 94.40% 3.30% 2.22% 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
vg0110837074 C -> T LOC_Os01g19170-LOC_Os01g19190 intergenic_region ; MODIFIER silent_mutation Average:67.373; most accessible tissue: Zhenshan97 flag leaf, score: 81.796 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0110837074 NA 2.23E-08 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
vg0110837074 NA 1.55E-07 mr1369 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
vg0110837074 NA 4.62E-06 mr1445 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
vg0110837074 NA 6.16E-09 mr1453 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
vg0110837074 8.78E-07 1.81E-13 mr1540 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
vg0110837074 NA 1.23E-07 mr1652 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
vg0110837074 4.49E-06 NA mr1732 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