| Variant ID: vg0817015825 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 17015825 |
| Reference Allele: A | Alternative Allele: C |
| Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
ATGCTCAATTTCAGCCCCAGCCACCAGCTGACAAGACAGAGGCCAGTATCTGCGTTGTACCTTTGGAAGTTCCAATACAGCAGCTGAGAAATCAAGTACA[A/C]
GATGAAGAACCCGAGTGTAAGAAAGTTATTGTTTGTTACAACTGCAATGAAGAAGGGCATTACTCCAAAAACTGTCCCCAACCAAGGCAAAATCGACCTC
GAGGTCGATTTTGCCTTGGTTGGGGACAGTTTTTGGAGTAATGCCCTTCTTCATTGCAGTTGTAACAAACAATAACTTTCTTACACTCGGGTTCTTCATC[T/G]
TGTACTTGATTTCTCAGCTGCTGTATTGGAACTTCCAAAGGTACAACGCAGATACTGGCCTCTGTCTTGTCAGCTGGTGGCTGGGGCTGAAATTGAGCAT
| 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 | 18.00% | 0.40% | 14.81% | 66.76% | NA |
| All Indica | 2759 | 2.00% | 0.60% | 13.05% | 84.31% | NA |
| All Japonica | 1512 | 50.30% | 0.00% | 13.16% | 36.57% | NA |
| Aus | 269 | 0.40% | 0.70% | 21.56% | 77.32% | NA |
| Indica I | 595 | 4.20% | 0.70% | 2.52% | 92.61% | NA |
| Indica II | 465 | 1.30% | 0.00% | 16.56% | 82.15% | NA |
| Indica III | 913 | 1.10% | 0.80% | 19.17% | 78.97% | NA |
| Indica Intermediate | 786 | 1.90% | 0.80% | 11.83% | 85.50% | NA |
| Temperate Japonica | 767 | 71.80% | 0.00% | 6.65% | 21.51% | NA |
| Tropical Japonica | 504 | 20.20% | 0.00% | 20.24% | 59.52% | NA |
| Japonica Intermediate | 241 | 44.40% | 0.00% | 19.09% | 36.51% | NA |
| VI/Aromatic | 96 | 11.50% | 0.00% | 64.58% | 23.96% | NA |
| Intermediate | 90 | 26.70% | 0.00% | 23.33% | 50.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0817015825 | A -> C | LOC_Os08g27910.1 | missense_variant ; p.Gln411His; MODERATE | nonsynonymous_codon ; Q411P | Average:5.953; most accessible tissue: Callus, score: 12.96 | unknown | unknown | TOLERATED | 0.17 |
| vg0817015825 | A -> DEL | LOC_Os08g27910.1 | N | frameshift_variant | Average:5.953; most accessible tissue: Callus, score: 12.96 | N | N | N | N |