| Variant ID: vg0136519513 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 36519513 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 54. )
ACTTAATGAAGAAACAATCAAGTAACATAGCATACGGATGGTTGACATACCTGTGACCCGACAGTTCCACGTACGTCTAACGAAGAGAAGTGTGATTCCA[A/G]
GAATTTTATTAAATTTTTACCGCCATCAATGGCTCTAGATGGGATCTTCGAACCGGAGCATAAGTTTAGGGGAGATAGCTCTGGCACATGGGGGTTGTTT
AAACAACCCCCATGTGCCAGAGCTATCTCCCCTAAACTTATGCTCCGGTTCGAAGATCCCATCTAGAGCCATTGATGGCGGTAAAAATTTAATAAAATTC[T/C]
TGGAATCACACTTCTCTTCGTTAGACGTACGTGGAACTGTCGGGTCACAGGTATGTCAACCATCCGTATGCTATGTTACTTGATTGTTTCTTCATTAAGT
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 9.10% | 2.50% | 20.40% | 67.99% | NA |
| All Indica | 2759 | 0.90% | 0.20% | 5.07% | 93.84% | NA |
| All Japonica | 1512 | 25.50% | 6.90% | 41.20% | 26.32% | NA |
| Aus | 269 | 0.40% | 0.00% | 42.01% | 57.62% | NA |
| Indica I | 595 | 0.20% | 0.00% | 2.69% | 97.14% | NA |
| Indica II | 465 | 1.70% | 0.00% | 3.87% | 94.41% | NA |
| Indica III | 913 | 0.50% | 0.10% | 4.27% | 95.07% | NA |
| Indica Intermediate | 786 | 1.40% | 0.50% | 8.52% | 89.57% | NA |
| Temperate Japonica | 767 | 42.40% | 3.50% | 28.68% | 25.42% | NA |
| Tropical Japonica | 504 | 5.00% | 13.30% | 55.75% | 25.99% | NA |
| Japonica Intermediate | 241 | 14.90% | 4.60% | 50.62% | 29.88% | NA |
| VI/Aromatic | 96 | 3.10% | 5.20% | 51.04% | 40.62% | NA |
| Intermediate | 90 | 15.60% | 5.60% | 43.33% | 35.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0136519513 | A -> G | LOC_Os01g63040.1 | synonymous_variant ; p.Leu408Leu; LOW | synonymous_codon | Average:5.165; most accessible tissue: Zhenshan97 root, score: 12.891 | N | N | N | N |
| vg0136519513 | A -> DEL | LOC_Os01g63040.1 | N | frameshift_variant | Average:5.165; most accessible tissue: Zhenshan97 root, score: 12.891 | N | N | N | N |