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Detailed information for vg0605440935:

Variant ID: vg0605440935 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 5440935
Reference Allele: TAlternative Allele: A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.79, T: 0.22, others allele: 0.00, population size: 213. )

Flanking Sequence (100 bp) in Reference Genome:


CTTTGGGTTGATGTCCAAATCGAAGTTCATAAGAAGTTTTTCCAAGTTTTGATCTCAAGAAAACCCGATTTGAAATATAACAAGCAGTGTTAATCGCCTC[T/A]
GCCCAAAATTTTCTTGGAGTTTTATATTCATCCAACATCGTTCTAGCCATCTCAACCAAAACATGGTTTTTCCTTTCAACAACACCGTTTTGTTGAGGAA

Reverse complement sequence

TTCCTCAACAAAACGGTGTTGTTGAAAGGAAAAACCATGTTTTGGTTGAGATGGCTAGAACGATGTTGGATGAATATAAAACTCCAAGAAAATTTTGGGC[A/T]
GAGGCGATTAACACTGCTTGTTATATTTCAAATCGGGTTTTCTTGAGATCAAAACTTGGAAAAACTTCTTATGAACTTCGATTTGGACATCAACCCAAAG

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 91.80% 8.10% 0.08% 0.00% NA
All Indica  2759 87.60% 12.40% 0.04% 0.00% NA
All Japonica  1512 99.50% 0.40% 0.13% 0.00% NA
Aus  269 91.10% 8.90% 0.00% 0.00% NA
Indica I  595 77.60% 22.40% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 85.80% 14.20% 0.00% 0.00% NA
Indica Intermediate  786 89.90% 9.90% 0.13% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 98.60% 1.00% 0.40% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 94.80% 5.20% 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
vg0605440935 T -> A LOC_Os06g10550.1 synonymous_variant ; p.Ala312Ala; LOW synonymous_codon Average:21.101; most accessible tissue: Zhenshan97 panicle, score: 32.308 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0605440935 2.28E-08 6.09E-19 mr1201 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
vg0605440935 6.27E-09 5.66E-18 mr1201 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
vg0605440935 5.91E-06 2.01E-12 mr1219 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
vg0605440935 3.47E-06 4.56E-14 mr1219 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
vg0605440935 1.52E-06 6.46E-15 mr1274 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
vg0605440935 9.33E-08 3.07E-15 mr1274 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
vg0605440935 1.76E-07 2.39E-15 mr1201_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
vg0605440935 2.61E-08 1.61E-14 mr1201_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
vg0605440935 NA 1.61E-09 mr1219_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
vg0605440935 NA 1.09E-10 mr1219_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
vg0605440935 NA 1.86E-13 mr1274_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
vg0605440935 NA 3.32E-13 mr1274_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