| Variant ID: vg0817015519 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 17015519 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 295. )
GAAACACAAATCCTCGCCAAGATTCCAGTTTCAGCCTAACTCCAGTGCCAGGACAGAGGAATCAAAATGAGAAAAGAAAATGCCGAGTCCGGGAAGATAT[C/T]
TGTTGCTTCAATTGTCAAGGAATGGGTCATTTCGCCGACAAGTGCCCAAAACCGAGAAACGTAGCTGCCAGCACGTCAGTCCACGCAAACCCCCGCAATC
GATTGCGGGGGTTTGCGTGGACTGACGTGCTGGCAGCTACGTTTCTCGGTTTTGGGCACTTGTCGGCGAAATGACCCATTCCTTGACAATTGAAGCAACA[G/A]
ATATCTTCCCGGACTCGGCATTTTCTTTTCTCATTTTGATTCCTCTGTCCTGGCACTGGAGTTAGGCTGAAACTGGAATCTTGGCGAGGATTTGTGTTTC
| 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 | 43.60% | 0.40% | 9.10% | 46.87% | NA |
| All Indica | 2759 | 32.30% | 0.00% | 11.34% | 56.36% | NA |
| All Japonica | 1512 | 64.20% | 1.30% | 2.05% | 32.41% | NA |
| Aus | 269 | 27.90% | 0.00% | 30.48% | 41.64% | NA |
| Indica I | 595 | 10.30% | 0.00% | 11.09% | 78.66% | NA |
| Indica II | 465 | 23.00% | 0.00% | 9.89% | 67.10% | NA |
| Indica III | 913 | 54.70% | 0.00% | 10.73% | 34.61% | NA |
| Indica Intermediate | 786 | 28.50% | 0.00% | 13.10% | 58.40% | NA |
| Temperate Japonica | 767 | 81.20% | 0.00% | 0.39% | 18.38% | NA |
| Tropical Japonica | 504 | 36.90% | 3.80% | 5.16% | 54.17% | NA |
| Japonica Intermediate | 241 | 67.20% | 0.40% | 0.83% | 31.54% | NA |
| VI/Aromatic | 96 | 79.20% | 0.00% | 0.00% | 20.83% | NA |
| Intermediate | 90 | 53.30% | 0.00% | 4.44% | 42.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0817015519 | C -> T | LOC_Os08g27910.1 | synonymous_variant ; p.Ile309Ile; LOW | synonymous_codon | Average:6.76; most accessible tissue: Minghui63 panicle, score: 16.27 | N | N | N | N |
| vg0817015519 | C -> DEL | LOC_Os08g27910.1 | N | frameshift_variant | Average:6.76; most accessible tissue: Minghui63 panicle, score: 16.27 | N | N | N | N |