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Detailed information for vg0107145470:

Variant ID: vg0107145470 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 7145470
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTACAGTAACCCGCATGTGCTAATGACGAAATAATTAGGCTTAATAAATTCGTCTTACGGTTTCTAGGCGAGTTATGAAATTAGTTTTTTCATTCGTGTC[C/T]
GAAAATACCTTTAGACATCCGATCAAATGTCCGATGTGACACCCAAAAATTTTCTTTTCGCGAACTAAACACACCCTAATTGTTTCTATGGCTCTAGTTT

Reverse complement sequence

AAACTAGAGCCATAGAAACAATTAGGGTGTGTTTAGTTCGCGAAAAGAAAATTTTTGGGTGTCACATCGGACATTTGATCGGATGTCTAAAGGTATTTTC[G/A]
GACACGAATGAAAAAACTAATTTCATAACTCGCCTAGAAACCGTAAGACGAATTTATTAAGCCTAATTATTTCGTCATTAGCACATGCGGGTTACTGTAG

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 81.80% 17.70% 0.42% 0.06% NA
All Indica  2759 69.90% 29.30% 0.72% 0.11% NA
All Japonica  1512 99.70% 0.30% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 91.40% 8.10% 0.50% 0.00% NA
Indica II  465 66.20% 33.80% 0.00% 0.00% NA
Indica III  913 66.30% 32.70% 0.77% 0.22% NA
Indica Intermediate  786 59.90% 38.70% 1.27% 0.13% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 99.40% 0.60% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 93.80% 6.20% 0.00% 0.00% NA
Intermediate  90 81.10% 18.90% 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
vg0107145470 C -> T LOC_Os01g12880-LOC_Os01g12890 intergenic_region ; MODIFIER silent_mutation Average:28.755; most accessible tissue: Zhenshan97 panicle, score: 52.263 N N N N
vg0107145470 C -> DEL N N silent_mutation Average:28.755; most accessible tissue: Zhenshan97 panicle, score: 52.263 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0107145470 NA 2.62E-07 mr1498 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
vg0107145470 3.22E-07 NA mr1699 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
vg0107145470 5.98E-07 1.24E-08 mr1699 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
vg0107145470 NA 1.07E-07 mr1925 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
vg0107145470 NA 2.41E-07 mr1951 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
vg0107145470 NA 3.09E-06 mr1310_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
vg0107145470 NA 9.73E-10 mr1498_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
vg0107145470 8.52E-09 NA mr1699_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
vg0107145470 1.10E-07 6.90E-13 mr1699_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