| Variant ID: vg0826585260 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 26585260 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 345. )
CATGTGAGTTATACTATGGTGGTAACCCAGTCTATGTGATCGGAGATCCCGTGAATTAGATCCTGGGAAGAACAAACCATTAATAAACTAGAGGAGAGTA[C/T]
CAATATATATACCCTCTCCAAGTGAAGATGCATATACTCTCGTGAGCTGCAAGGCAGGTTGGCTATGCCTTAATGAGTTCTGTTGGCTTTAATTAGCAAA
TTTGCTAATTAAAGCCAACAGAACTCATTAAGGCATAGCCAACCTGCCTTGCAGCTCACGAGAGTATATGCATCTTCACTTGGAGAGGGTATATATATTG[G/A]
TACTCTCCTCTAGTTTATTAATGGTTTGTTCTTCCCAGGATCTAATTCACGGGATCTCCGATCACATAGACTGGGTTACCACCATAGTATAACTCACATG
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 29.70% | 0.10% | 21.29% | 48.94% | NA |
| All Indica | 2759 | 1.30% | 0.00% | 33.09% | 65.64% | NA |
| All Japonica | 1512 | 80.70% | 0.30% | 1.72% | 17.26% | NA |
| Aus | 269 | 8.20% | 0.00% | 18.22% | 73.61% | NA |
| Indica I | 595 | 0.50% | 0.00% | 22.35% | 77.14% | NA |
| Indica II | 465 | 1.30% | 0.00% | 24.95% | 73.76% | NA |
| Indica III | 913 | 0.80% | 0.00% | 47.75% | 51.48% | NA |
| Indica Intermediate | 786 | 2.40% | 0.00% | 29.01% | 68.58% | NA |
| Temperate Japonica | 767 | 93.90% | 0.40% | 0.65% | 5.08% | NA |
| Tropical Japonica | 504 | 70.20% | 0.00% | 3.37% | 26.39% | NA |
| Japonica Intermediate | 241 | 60.60% | 0.80% | 1.66% | 36.93% | NA |
| VI/Aromatic | 96 | 92.70% | 0.00% | 1.04% | 6.25% | NA |
| Intermediate | 90 | 40.00% | 0.00% | 18.89% | 41.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0826585260 | C -> T | LOC_Os08g42090.1 | intron_variant ; MODIFIER | silent_mutation | Average:6.945; most accessible tissue: Minghui63 young leaf, score: 11.521 | N | N | N | N |
| vg0826585260 | C -> DEL | N | N | silent_mutation | Average:6.945; most accessible tissue: Minghui63 young leaf, score: 11.521 | N | N | N | N |