| Variant ID: vg0817015584 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 17015584 |
| 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: 295. )
AATGAGAAAAGAAAATGCCGAGTCCGGGAAGATATCTGTTGCTTCAATTGTCAAGGAATGGGTCATTTCGCCGACAAGTGCCCAAAACCGAGAAACGTAG[C/T]
TGCCAGCACGTCAGTCCACGCAAACCCCCGCAATCAGAAGCTTGCTCCTCAACGAATTGTCATCCATGCATCCCGAAGCAGTCCGATAGCCCGCGTTGCA
TGCAACGCGGGCTATCGGACTGCTTCGGGATGCATGGATGACAATTCGTTGAGGAGCAAGCTTCTGATTGCGGGGGTTTGCGTGGACTGACGTGCTGGCA[G/A]
CTACGTTTCTCGGTTTTGGGCACTTGTCGGCGAAATGACCCATTCCTTGACAATTGAAGCAACAGATATCTTCCCGGACTCGGCATTTTCTTTTCTCATT
| 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 | 23.00% | 1.10% | 25.10% | 50.78% | NA |
| All Indica | 2759 | 9.80% | 0.00% | 27.18% | 62.96% | NA |
| All Japonica | 1512 | 48.50% | 3.20% | 16.27% | 31.94% | NA |
| Aus | 269 | 16.00% | 0.00% | 39.03% | 44.98% | NA |
| Indica I | 595 | 5.90% | 0.20% | 9.41% | 84.54% | NA |
| Indica II | 465 | 1.50% | 0.00% | 24.52% | 73.98% | NA |
| Indica III | 913 | 17.60% | 0.00% | 40.53% | 41.84% | NA |
| Indica Intermediate | 786 | 8.70% | 0.00% | 26.72% | 64.63% | NA |
| Temperate Japonica | 767 | 70.50% | 0.50% | 10.69% | 18.25% | NA |
| Tropical Japonica | 504 | 20.20% | 7.30% | 19.25% | 53.17% | NA |
| Japonica Intermediate | 241 | 37.80% | 3.30% | 27.80% | 31.12% | NA |
| VI/Aromatic | 96 | 13.50% | 0.00% | 65.62% | 20.83% | NA |
| Intermediate | 90 | 30.00% | 2.20% | 24.44% | 43.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0817015584 | C -> T | LOC_Os08g27910.1 | missense_variant ; p.Ala331Val; MODERATE | nonsynonymous_codon ; A331V | Average:6.759; most accessible tissue: Minghui63 panicle, score: 16.27 | unknown | unknown | DELETERIOUS | 0.03 |
| vg0817015584 | C -> DEL | LOC_Os08g27910.1 | N | frameshift_variant | Average:6.759; most accessible tissue: Minghui63 panicle, score: 16.27 | N | N | N | N |