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Detailed information for vg0319023759:

Variant ID: vg0319023759 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 19023759
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, others allele: 0.00, population size: 53. )

Flanking Sequence (100 bp) in Reference Genome:


ATGCAGTTACAACACTTTTTCCTTTGGCCAATCTCTTTGCTTCATCGGTCGTGGCTTCATCGGCTGCAGGAACCTGATTTTTAACACGCCACTCCTGCCT[T/C]
GGCTTTGTTTTCTTTAGCCGATGACTGATTTCCTGTTCAACCTCCTGAAAACGTTCCCGGTTCCTTAATCTCTGAACCCTTCTCTTCTGATTTTTTGTAA

Reverse complement sequence

TTACAAAAAATCAGAAGAGAAGGGTTCAGAGATTAAGGAACCGGGAACGTTTTCAGGAGGTTGAACAGGAAATCAGTCATCGGCTAAAGAAAACAAAGCC[A/G]
AGGCAGGAGTGGCGTGTTAAAAATCAGGTTCCTGCAGCCGATGAAGCCACGACCGATGAAGCAAAGAGATTGGCCAAAGGAAAAAGTGTTGTAACTGCAT

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 76.30% 10.70% 2.77% 10.22% NA
All Indica  2759 80.10% 1.20% 2.36% 16.38% NA
All Japonica  1512 64.10% 30.30% 4.10% 1.52% NA
Aus  269 98.90% 0.00% 0.37% 0.74% NA
Indica I  595 92.40% 0.70% 3.70% 3.19% NA
Indica II  465 75.50% 2.80% 2.15% 19.57% NA
Indica III  913 71.20% 0.70% 0.88% 27.27% NA
Indica Intermediate  786 83.70% 1.30% 3.18% 11.83% NA
Temperate Japonica  767 43.40% 50.60% 6.00% 0.00% NA
Tropical Japonica  504 91.90% 6.90% 0.79% 0.40% NA
Japonica Intermediate  241 71.80% 14.50% 4.98% 8.71% NA
VI/Aromatic  96 94.80% 1.00% 1.04% 3.12% NA
Intermediate  90 81.10% 13.30% 2.22% 3.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0319023759 T -> C LOC_Os03g33250.1 synonymous_variant ; p.Pro66Pro; LOW synonymous_codon Average:19.037; most accessible tissue: Zhenshan97 panicle, score: 36.038 N N N N
vg0319023759 T -> DEL LOC_Os03g33250.1 N frameshift_variant Average:19.037; most accessible tissue: Zhenshan97 panicle, score: 36.038 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0319023759 NA 3.90E-11 Heading_date 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
vg0319023759 NA 1.45E-09 Heading_date Jap_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
vg0319023759 NA 1.74E-13 Plant_height Jap_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
vg0319023759 2.42E-07 NA mr1354 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
vg0319023759 NA 6.70E-06 mr1354 Jap_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
vg0319023759 NA 1.51E-09 mr1002_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
vg0319023759 NA 6.99E-07 mr1321_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
vg0319023759 NA 5.41E-08 mr1576_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
vg0319023759 NA 4.43E-06 mr1576_2 Jap_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
vg0319023759 NA 4.07E-06 mr1648_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
vg0319023759 NA 3.69E-08 mr1709_2 Jap_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