| Variant ID: vg0142999351 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 42999351 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CCTCGGGGATCGAGACGGGCTCGGGAGCCGGGGTCCACTCTGCCACAAAATCGGCGAGGGCCTGGCTCTTGATAGCGTGGCGTGGTTCAAAGTGCAAATC[G/A]
AACTCAGAAAGTTCGATTGCCCATTTCACCACCCGTCCTGTACCCTCTTGATTATGCAAGATTTGACCGAGGGGGTAAGACGTAACTACTGTGACCCGAT
ATCGGGTCACAGTAGTTACGTCTTACCCCCTCGGTCAAATCTTGCATAATCAAGAGGGTACAGGACGGGTGGTGAAATGGGCAATCGAACTTTCTGAGTT[C/T]
GATTTGCACTTTGAACCACGCCACGCTATCAAGAGCCAGGCCCTCGCCGATTTTGTGGCAGAGTGGACCCCGGCTCCCGAGCCCGTCTCGATCCCCGAGG
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 6.90% | 0.10% | 2.71% | 90.29% | NA |
| All Indica | 2759 | 0.40% | 0.20% | 2.79% | 96.67% | NA |
| All Japonica | 1512 | 20.00% | 0.00% | 0.99% | 78.97% | NA |
| Aus | 269 | 0.40% | 0.00% | 13.38% | 86.25% | NA |
| Indica I | 595 | 0.30% | 0.00% | 0.67% | 98.99% | NA |
| Indica II | 465 | 0.40% | 0.00% | 0.65% | 98.92% | NA |
| Indica III | 913 | 0.00% | 0.30% | 4.82% | 94.85% | NA |
| Indica Intermediate | 786 | 0.80% | 0.30% | 3.31% | 95.67% | NA |
| Temperate Japonica | 767 | 37.90% | 0.00% | 1.04% | 61.02% | NA |
| Tropical Japonica | 504 | 0.80% | 0.00% | 0.60% | 98.61% | NA |
| Japonica Intermediate | 241 | 3.30% | 0.00% | 1.66% | 95.02% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 0.00% | 100.00% | NA |
| Intermediate | 90 | 13.30% | 0.00% | 0.00% | 86.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0142999351 | G -> A | LOC_Os01g74230.1 | synonymous_variant ; p.Phe1217Phe; LOW | synonymous_codon | Average:7.742; most accessible tissue: Callus, score: 13.366 | N | N | N | N |
| vg0142999351 | G -> DEL | LOC_Os01g74230.1 | N | frameshift_variant | Average:7.742; most accessible tissue: Callus, score: 13.366 | N | N | N | N |