| Variant ID: vg1101256047 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 1256047 |
| Reference Allele: C | Alternative Allele: G |
| Primary Allele: C | Secondary Allele: G |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 263. )
GTGATGATGTCCCCTCTCTTTCCAGTATGTTCTATGCATTTTACTTGACTTATATTTGCCCAAAATGAGTCCGTTTGTTAACTAAATACAGGCAATGAGC[C/G]
TTAGAAACTCTCGGAACAGAGCAGGCTTAAAAATGCCTCATCGCACTGGAAGCAAACCCTTCAGAGAGATAATCTACAATATGGTATAAATAAAAGAATT
AATTCTTTTATTTATACCATATTGTAGATTATCTCTCTGAAGGGTTTGCTTCCAGTGCGATGAGGCATTTTTAAGCCTGCTCTGTTCCGAGAGTTTCTAA[G/C]
GCTCATTGCCTGTATTTAGTTAACAAACGGACTCATTTTGGGCAAATATAAGTCAAGTAAAATGCATAGAACATACTGGAAAGAGAGGGGACATCATCAC
| Populations | Population Size | Frequency of C(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 70.50% | 0.10% | 0.68% | 28.73% | NA |
| All Indica | 2759 | 54.80% | 0.20% | 0.76% | 44.26% | NA |
| All Japonica | 1512 | 97.90% | 0.00% | 0.00% | 2.05% | NA |
| Aus | 269 | 76.60% | 0.00% | 2.60% | 20.82% | NA |
| Indica I | 595 | 26.20% | 0.00% | 1.01% | 72.77% | NA |
| Indica II | 465 | 52.00% | 0.00% | 0.65% | 47.31% | NA |
| Indica III | 913 | 71.90% | 0.50% | 0.55% | 27.05% | NA |
| Indica Intermediate | 786 | 58.30% | 0.00% | 0.89% | 40.84% | NA |
| Temperate Japonica | 767 | 98.60% | 0.00% | 0.00% | 1.43% | NA |
| Tropical Japonica | 504 | 97.80% | 0.00% | 0.00% | 2.18% | NA |
| Japonica Intermediate | 241 | 96.30% | 0.00% | 0.00% | 3.73% | NA |
| VI/Aromatic | 96 | 68.80% | 0.00% | 4.17% | 27.08% | NA |
| Intermediate | 90 | 73.30% | 0.00% | 0.00% | 26.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1101256047 | C -> DEL | LOC_Os11g03340.1 | N | frameshift_variant | Average:4.744; most accessible tissue: Callus, score: 7.517 | N | N | N | N |
| vg1101256047 | C -> G | LOC_Os11g03340.1 | missense_variant ; p.Leu265Val; MODERATE | nonsynonymous_codon ; L265V | Average:4.744; most accessible tissue: Callus, score: 7.517 | unknown | unknown | TOLERATED | 0.32 |