| Variant ID: vg0817014780 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 17014780 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 286. )
TGTGTGGCAGTGGTCCAACACCTGATTAACCAGAACAAATTGCTTATAGAGATACTACAGCAGCATCGGATGCCAATTTTGAACCCGAGTCAGATGCAAC[C/T]
TCAAGTGCAGTTGGAGGCAGTCCAAGCACTCACACCACAAGTCAGCGCACCGCCAACATCCCAGAAGGCCCCTCATGCCATGCCACATGTTGACCCAAAA
TTTTGGGTCAACATGTGGCATGGCATGAGGGGCCTTCTGGGATGTTGGCGGTGCGCTGACTTGTGGTGTGAGTGCTTGGACTGCCTCCAACTGCACTTGA[G/A]
GTTGCATCTGACTCGGGTTCAAAATTGGCATCCGATGCTGCTGTAGTATCTCTATAAGCAATTTGTTCTGGTTAATCAGGTGTTGGACCACTGCCACACA
| 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 | 56.10% | 0.10% | 1.69% | 42.09% | NA |
| All Indica | 2759 | 48.50% | 0.10% | 1.96% | 49.40% | NA |
| All Japonica | 1512 | 66.80% | 0.00% | 1.46% | 31.75% | NA |
| Aus | 269 | 65.40% | 0.00% | 1.12% | 33.46% | NA |
| Indica I | 595 | 26.60% | 0.00% | 2.02% | 71.43% | NA |
| Indica II | 465 | 38.30% | 0.00% | 1.51% | 60.22% | NA |
| Indica III | 913 | 69.40% | 0.40% | 2.52% | 27.60% | NA |
| Indica Intermediate | 786 | 46.80% | 0.00% | 1.53% | 51.65% | NA |
| Temperate Japonica | 767 | 79.90% | 0.00% | 1.69% | 18.38% | NA |
| Tropical Japonica | 504 | 46.00% | 0.00% | 1.59% | 52.38% | NA |
| Japonica Intermediate | 241 | 68.50% | 0.00% | 0.41% | 31.12% | NA |
| VI/Aromatic | 96 | 79.20% | 0.00% | 0.00% | 20.83% | NA |
| Intermediate | 90 | 58.90% | 0.00% | 1.11% | 40.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0817014780 | C -> T | LOC_Os08g27910.1 | missense_variant ; p.Pro63Leu; MODERATE | nonsynonymous_codon ; P63L | Average:4.677; most accessible tissue: Minghui63 panicle, score: 7.125 | unknown | unknown | DELETERIOUS | 0.00 |
| vg0817014780 | C -> DEL | LOC_Os08g27910.1 | N | frameshift_variant | Average:4.677; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |