| Variant ID: vg0106163187 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 6163187 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.01, others allele: 0.00, population size: 286. )
TATCTGGTACTAGACCGTCTGTAGACTACCCCTCGGGTGGAGCGTATAAGTCATACTCCTAGGTCTTTAGTAAGCTTCCTAGAAGATTCACCCAAAATCT[T/C]
CATAGACTGCGACCAACAGTCAAGCTCACAAAGGTGAGTTCTTTCAAGAATGCTCTGCAGGACAATATATTTGCTAATTAAAGCCAACAGAACTCATTAA
TTAATGAGTTCTGTTGGCTTTAATTAGCAAATATATTGTCCTGCAGAGCATTCTTGAAAGAACTCACCTTTGTGAGCTTGACTGTTGGTCGCAGTCTATG[A/G]
AGATTTTGGGTGAATCTTCTAGGAAGCTTACTAAAGACCTAGGAGTATGACTTATACGCTCCACCCGAGGGGTAGTCTACAGACGGTCTAGTACCAGATA
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 22.50% | 0.10% | 2.43% | 74.99% | NA |
| All Indica | 2759 | 1.00% | 0.00% | 2.75% | 96.23% | NA |
| All Japonica | 1512 | 64.40% | 0.00% | 0.53% | 35.12% | NA |
| Aus | 269 | 0.00% | 1.10% | 9.67% | 89.22% | NA |
| Indica I | 595 | 0.20% | 0.00% | 0.17% | 99.66% | NA |
| Indica II | 465 | 0.90% | 0.00% | 1.51% | 97.63% | NA |
| Indica III | 913 | 0.90% | 0.00% | 4.71% | 94.41% | NA |
| Indica Intermediate | 786 | 1.80% | 0.10% | 3.18% | 94.91% | NA |
| Temperate Japonica | 767 | 95.00% | 0.00% | 0.13% | 4.82% | NA |
| Tropical Japonica | 504 | 29.60% | 0.00% | 1.39% | 69.05% | NA |
| Japonica Intermediate | 241 | 39.40% | 0.00% | 0.00% | 60.58% | NA |
| VI/Aromatic | 96 | 41.70% | 0.00% | 2.08% | 56.25% | NA |
| Intermediate | 90 | 24.40% | 1.10% | 3.33% | 71.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0106163187 | T -> DEL | LOC_Os01g11450.1 | N | frameshift_variant | Average:5.697; most accessible tissue: Zhenshan97 root, score: 10.511 | N | N | N | N |
| vg0106163187 | T -> C | LOC_Os01g11450.1 | stop_lost&splice_region_variant ; p.Ter891Trpext*?; HIGH | stop_lost | Average:5.697; most accessible tissue: Zhenshan97 root, score: 10.511 | N | N | N | N |