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Detailed information for vg0103148298:

Variant ID: vg0103148298 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 3148298
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:


TCTCCGACACATCCCCCCATTGCTCGATGGTGCTTATGAGGGGTTGGAACTTGTCGGGAACGGAATGCAAGAGCTTCTCCACCACCGTGGTCTCCTCCAC[T/C]
TTCGTGCCGAGAGAGCGAATCTCGTTCACGATCGTGGTAACCTTTAAAGCAAAATCATTAATTTTCTCAGAATTACTCATGTACATACCATCAAGCTCCC

Reverse complement sequence

GGGAGCTTGATGGTATGTACATGAGTAATTCTGAGAAAATTAATGATTTTGCTTTAAAGGTTACCACGATCGTGAACGAGATTCGCTCTCTCGGCACGAA[A/G]
GTGGAGGAGACCACGGTGGTGGAGAAGCTCTTGCATTCCGTTCCCGACAAGTTCCAACCCCTCATAAGCACCATCGAGCAATGGGGGGATGTGTCGGAGA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 59.70% 12.20% 3.11% 24.97% NA
All Indica  2759 75.10% 2.00% 2.25% 20.66% NA
All Japonica  1512 22.00% 33.90% 5.36% 38.76% NA
Aus  269 96.70% 0.00% 0.00% 3.35% NA
Indica I  595 94.80% 0.00% 0.34% 4.87% NA
Indica II  465 77.60% 2.20% 1.08% 19.14% NA
Indica III  913 66.30% 2.20% 3.72% 27.82% NA
Indica Intermediate  786 69.10% 3.10% 2.67% 25.19% NA
Temperate Japonica  767 29.20% 13.30% 1.56% 55.93% NA
Tropical Japonica  504 11.50% 58.90% 9.52% 20.04% NA
Japonica Intermediate  241 21.20% 46.90% 8.71% 23.24% NA
VI/Aromatic  96 94.80% 1.00% 0.00% 4.17% NA
Intermediate  90 73.30% 10.00% 4.44% 12.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0103148298 T -> DEL LOC_Os01g06680.1 N frameshift_variant Average:57.3; most accessible tissue: Callus, score: 95.813 N N N N
vg0103148298 T -> C LOC_Os01g06680.1 synonymous_variant ; p.Lys654Lys; LOW synonymous_codon Average:57.3; most accessible tissue: Callus, score: 95.813 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0103148298 NA 8.31E-07 mr1245 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
vg0103148298 NA 1.89E-06 mr1392 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
vg0103148298 9.02E-07 NA mr1403 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
vg0103148298 5.61E-06 NA mr1403 Jap_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
vg0103148298 NA 7.94E-07 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
vg0103148298 NA 1.16E-11 mr1636 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
vg0103148298 NA 3.78E-11 mr1751 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
vg0103148298 NA 2.96E-08 mr1779 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