Search for Variation information by Variation ID:
Detailed information for vg0719818719:
| Variant ID: vg0719818719 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 19818719 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 88. )
Flanking Sequence (100 bp) in Reference Genome:
CCACCGAGATCCTCGAGTTCTTCTCCCATCAAGAAGGCACTTCAGGCAATCTTCTGTATGTGTGCTAAAACTGCTATGAAAGTGAAGAAGATTGAAAGGC[A/G]
TCAGAAGGAAGATAGAAGAGAGGTTGGGAAAGAAGTGTCAGATGATTCTGAAGATGAGGTCTATGTTGATCCATTTGAGGCTTATGAGGCAGCCCGCAAC
Reverse complement sequence
GTTGCGGGCTGCCTCATAAGCCTCAAATGGATCAACATAGACCTCATCTTCAGAATCATCTGACACTTCTTTCCCAACCTCTCTTCTATCTTCCTTCTGA[T/C]
GCCTTTCAATCTTCTTCACTTTCATAGCAGTTTTAGCACACATACAGAAGATTGCCTGAAGTGCCTTCTTGATGGGAGAAGAACTCGAGGATCTCGGTGG
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 28.40% | 14.80% | 0.66% | 56.20% | NA |
| All Indica | 2759 | 8.70% | 2.50% | 0.91% | 87.93% | NA |
| All Japonica | 1512 | 48.60% | 40.60% | 0.26% | 10.52% | NA |
| Aus | 269 | 88.80% | 0.00% | 0.00% | 11.15% | NA |
| Indica I | 595 | 0.70% | 4.20% | 1.51% | 93.61% | NA |
| Indica II | 465 | 4.50% | 3.00% | 0.43% | 92.04% | NA |
| Indica III | 913 | 15.70% | 0.80% | 0.33% | 83.24% | NA |
| Indica Intermediate | 786 | 9.00% | 2.90% | 1.40% | 86.64% | NA |
| Temperate Japonica | 767 | 45.80% | 52.90% | 0.13% | 1.17% | NA |
| Tropical Japonica | 504 | 58.50% | 12.10% | 0.60% | 28.77% | NA |
| Japonica Intermediate | 241 | 36.90% | 61.00% | 0.00% | 2.07% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 35.60% | 16.70% | 2.22% | 45.56% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0719818719 | A -> DEL | LOC_Os07g33190.1 | N | frameshift_variant | Average:13.172; most accessible tissue: Callus, score: 30.303 | N | N | N | N |
| vg0719818719 | A -> G | LOC_Os07g33190.1 | missense_variant ; p.His887Arg; MODERATE | nonsynonymous_codon ; H887R | Average:13.172; most accessible tissue: Callus, score: 30.303 | possibly damaging  |
-1.872 |
TOLERATED | 1.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0719818719 | 9.54E-06 | NA | Spikelet_length | 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 |
| vg0719818719 | 1.62E-06 | 2.19E-06 | mr1210 | 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 |
| vg0719818719 | NA | 4.90E-09 | 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 |
| vg0719818719 | NA | 4.78E-09 | mr1821_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 |