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Detailed information for vg0501221925:

Variant ID: vg0501221925 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 1221925
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AGATATTTCAAAGGAGGAATCAAAAGGTGCACTTACCTGTTGATTTTTCCTGCTCTTCACCTTTTTCCTTCTCCAAATCGCTCAAACTTGTGATTCCTTT[C/T]
TGTGTGTACTGTAAATTTGCTTCTCTATCGTCAATTTTCTCGTTAATCTCCATCTTTTTTTCTTCTGACTTCAGATCTGTCTCTGTTTGATTCCCCCTAT

Reverse complement sequence

ATAGGGGGAATCAAACAGAGACAGATCTGAAGTCAGAAGAAAAAAAGATGGAGATTAACGAGAAAATTGACGATAGAGAAGCAAATTTACAGTACACACA[G/A]
AAAGGAATCACAAGTTTGAGCGATTTGGAGAAGGAAAAAGGTGAAGAGCAGGAAAAATCAACAGGTAAGTGCACCTTTTGATTCCTCCTTTGAAATATCT

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 90.30% 9.60% 0.13% 0.00% NA
All Indica  2759 91.20% 8.80% 0.00% 0.00% NA
All Japonica  1512 99.80% 0.10% 0.07% 0.00% NA
Aus  269 24.50% 73.60% 1.86% 0.00% NA
Indica I  595 96.60% 3.40% 0.00% 0.00% NA
Indica II  465 95.30% 4.70% 0.00% 0.00% NA
Indica III  913 85.00% 15.00% 0.00% 0.00% NA
Indica Intermediate  786 91.90% 8.10% 0.00% 0.00% NA
Temperate Japonica  767 99.70% 0.10% 0.13% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 91.70% 8.30% 0.00% 0.00% NA
Intermediate  90 97.80% 2.20% 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
vg0501221925 C -> T LOC_Os05g03090.1 synonymous_variant ; p.Gln18Gln; LOW synonymous_codon Average:50.21; most accessible tissue: Zhenshan97 flower, score: 80.463 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0501221925 NA 4.13E-07 mr1807 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
vg0501221925 NA 5.46E-06 mr1096_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
vg0501221925 NA 5.11E-07 mr1098_2 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
vg0501221925 9.03E-06 NA mr1123_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
vg0501221925 NA 1.69E-06 mr1144_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
vg0501221925 NA 3.11E-07 mr1676_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
vg0501221925 NA 2.35E-09 mr1970_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
vg0501221925 NA 5.84E-10 mr1973_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