| Variant ID: vg0817015824 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 17015824 |
| Reference Allele: A | Alternative Allele: C |
| Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
AATGCTCAATTTCAGCCCCAGCCACCAGCTGACAAGACAGAGGCCAGTATCTGCGTTGTACCTTTGGAAGTTCCAATACAGCAGCTGAGAAATCAAGTAC[A/C]
AGATGAAGAACCCGAGTGTAAGAAAGTTATTGTTTGTTACAACTGCAATGAAGAAGGGCATTACTCCAAAAACTGTCCCCAACCAAGGCAAAATCGACCT
AGGTCGATTTTGCCTTGGTTGGGGACAGTTTTTGGAGTAATGCCCTTCTTCATTGCAGTTGTAACAAACAATAACTTTCTTACACTCGGGTTCTTCATCT[T/G]
GTACTTGATTTCTCAGCTGCTGTATTGGAACTTCCAAAGGTACAACGCAGATACTGGCCTCTGTCTTGTCAGCTGGTGGCTGGGGCTGAAATTGAGCATT
| Populations | Population Size | Frequency of A(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 17.80% | 0.40% | 12.67% | 69.13% | NA |
| All Indica | 2759 | 1.90% | 0.60% | 10.91% | 86.55% | NA |
| All Japonica | 1512 | 50.00% | 0.00% | 13.03% | 36.97% | NA |
| Aus | 269 | 0.40% | 0.70% | 8.92% | 89.96% | NA |
| Indica I | 595 | 4.00% | 0.70% | 2.18% | 93.11% | NA |
| Indica II | 465 | 1.30% | 0.00% | 14.84% | 83.87% | NA |
| Indica III | 913 | 1.00% | 0.80% | 16.98% | 81.27% | NA |
| Indica Intermediate | 786 | 1.80% | 0.80% | 8.14% | 89.31% | NA |
| Temperate Japonica | 767 | 71.60% | 0.00% | 6.91% | 21.51% | NA |
| Tropical Japonica | 504 | 20.20% | 0.00% | 19.05% | 60.71% | NA |
| Japonica Intermediate | 241 | 43.60% | 0.00% | 19.92% | 36.51% | NA |
| VI/Aromatic | 96 | 8.30% | 0.00% | 64.58% | 27.08% | NA |
| Intermediate | 90 | 25.60% | 0.00% | 16.67% | 57.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0817015824 | A -> C | LOC_Os08g27910.1 | missense_variant ; p.Gln411Pro; MODERATE | nonsynonymous_codon ; Q411P | Average:5.953; most accessible tissue: Callus, score: 12.96 | unknown | unknown | TOLERATED | 0.17 |
| vg0817015824 | A -> DEL | LOC_Os08g27910.1 | N | frameshift_variant | Average:5.953; most accessible tissue: Callus, score: 12.96 | N | N | N | N |