| Variant ID: vg0817014770 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 17014770 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 277. )
AGACACCAGTTGTGTGGCAGTGGTCCAACACCTGATTAACCAGAACAAATTGCTTATAGAGATACTACAGCAGCATCGGATGCCAATTTTGAACCCGAGT[C/A]
AGATGCAACCTCAAGTGCAGTTGGAGGCAGTCCAAGCACTCACACCACAAGTCAGCGCACCGCCAACATCCCAGAAGGCCCCTCATGCCATGCCACATGT
ACATGTGGCATGGCATGAGGGGCCTTCTGGGATGTTGGCGGTGCGCTGACTTGTGGTGTGAGTGCTTGGACTGCCTCCAACTGCACTTGAGGTTGCATCT[G/T]
ACTCGGGTTCAAAATTGGCATCCGATGCTGCTGTAGTATCTCTATAAGCAATTTGTTCTGGTTAATCAGGTGTTGGACCACTGCCACACAACTGGTGTCT
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 56.40% | 0.10% | 1.63% | 41.90% | NA |
| All Indica | 2759 | 48.80% | 0.10% | 1.96% | 49.11% | NA |
| All Japonica | 1512 | 66.90% | 0.00% | 1.32% | 31.75% | NA |
| Aus | 269 | 65.80% | 0.00% | 1.12% | 33.09% | NA |
| Indica I | 595 | 26.70% | 0.00% | 2.18% | 71.09% | NA |
| Indica II | 465 | 38.30% | 0.00% | 1.51% | 60.22% | NA |
| Indica III | 913 | 70.10% | 0.40% | 2.19% | 27.27% | NA |
| Indica Intermediate | 786 | 46.90% | 0.00% | 1.78% | 51.27% | NA |
| Temperate Japonica | 767 | 79.90% | 0.00% | 1.69% | 18.38% | NA |
| Tropical Japonica | 504 | 46.40% | 0.00% | 1.19% | 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 | 60.00% | 0.00% | 0.00% | 40.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0817014770 | C -> A | LOC_Os08g27910.1 | missense_variant ; p.Gln60Lys; MODERATE | nonsynonymous_codon ; Q60K | Average:5.547; most accessible tissue: Zhenshan97 flower, score: 9.663 | unknown | unknown | TOLERATED | 0.19 |
| vg0817014770 | C -> DEL | LOC_Os08g27910.1 | N | frameshift_variant | Average:5.547; most accessible tissue: Zhenshan97 flower, score: 9.663 | N | N | N | N |