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Detailed information for vg0610191856:

Variant ID: vg0610191856 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 10191856
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.02, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:


ATTATTTCCACTTCCCATTTGTCTTTTTGATTAAGCAAATGTATTTTGAGACAGTAATCCCCGATTTCCACTTTTTGGACCAAGCACTAGTTCTTATCAA[C/T]
AGAGAATTCCCCTAGATCTCCCTCTAGCAGGTAACAAGGTCCAATCAAACAATTTCTTTCCACTTATATAATTCAGGAGATTATTGTTGAAATCCTATTT

Reverse complement sequence

AAATAGGATTTCAACAATAATCTCCTGAATTATATAAGTGGAAAGAAATTGTTTGATTGGACCTTGTTACCTGCTAGAGGGAGATCTAGGGGAATTCTCT[G/A]
TTGATAAGAACTAGTGCTTGGTCCAAAAAGTGGAAATCGGGGATTACTGTCTCAAAATACATTTGCTTAATCAAAAAGACAAATGGGAAGTGGAAATAAT

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 86.40% 11.60% 2.03% 0.00% NA
All Indica  2759 78.30% 18.30% 3.44% 0.00% NA
All Japonica  1512 98.10% 1.90% 0.07% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 48.60% 40.50% 10.92% 0.00% NA
Indica II  465 85.40% 11.80% 2.80% 0.00% NA
Indica III  913 86.60% 13.30% 0.11% 0.00% NA
Indica Intermediate  786 86.90% 11.10% 2.04% 0.00% NA
Temperate Japonica  767 97.80% 2.10% 0.13% 0.00% NA
Tropical Japonica  504 99.40% 0.60% 0.00% 0.00% NA
Japonica Intermediate  241 96.30% 3.70% 0.00% 0.00% NA
VI/Aromatic  96 91.70% 8.30% 0.00% 0.00% NA
Intermediate  90 92.20% 7.80% 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
vg0610191856 C -> T LOC_Os06g17560-LOC_Os06g17570 intergenic_region ; MODIFIER silent_mutation Average:29.152; most accessible tissue: Callus, score: 43.584 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0610191856 NA 3.74E-10 Heading_date Ind_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0610191856 1.99E-06 NA mr1695 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
vg0610191856 3.04E-06 NA mr1695 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
vg0610191856 NA 2.33E-07 mr1215_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
vg0610191856 NA 6.11E-06 mr1220_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
vg0610191856 NA 1.53E-09 mr1221_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
vg0610191856 NA 8.27E-06 mr1422_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
vg0610191856 NA 3.07E-08 mr1583_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
vg0610191856 1.05E-06 NA mr1695_2 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
vg0610191856 6.77E-06 NA mr1695_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
vg0610191856 NA 2.46E-06 mr1968_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