| Variant ID: vg0132053221 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr01 | Position: 32053221 |
| Reference Allele: GAT | Alternative Allele: G,GATAT |
| Primary Allele: G | Secondary Allele: GAT |
Inferred Ancestral Allele: Not determined.
CCATCGTTTCAGATAGGGAGATGTTGTTGCATTGCCTGCTGGTGTAGCTCATTGGTGCTACAATGATGGTGATGTACCAATTGTTGCCATATACGTCACT[GAT/G,GATAT]
ATATATATAACAGTGCTAACCAGCTTGATCCTAGAAAAAAGGTAATTAATCATAGCTTATTTATTGCCAACAACCCAAGCATTCTTTGAATTCGTTTGAT
ATCAAACGAATTCAAAGAATGCTTGGGTTGTTGGCAATAAATAAGCTATGATTAATTACCTTTTTTCTAGGATCAAGCTGGTTAGCACTGTTATATATAT[ATC/C,ATATC]
AGTGACGTATATGGCAACAATTGGTACATCACCATCATTGTAGCACCAATGAGCTACACCAGCAGGCAATGCAACAACATCTCCCTATCTGAAACGATGG
| Populations | Population Size | Frequency of G(primary allele) | Frequency of GAT(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 79.20% | 20.80% | 0.00% | 0.00% | GATAT: 0.04% |
| All Indica | 2759 | 98.10% | 1.90% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 40.50% | 59.40% | 0.00% | 0.00% | GATAT: 0.13% |
| Aus | 269 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica I | 595 | 97.00% | 3.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 98.90% | 1.10% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 96.30% | 3.70% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 4.20% | 95.60% | 0.00% | 0.00% | GATAT: 0.26% |
| Tropical Japonica | 504 | 89.90% | 10.10% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 52.70% | 47.30% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 89.60% | 10.40% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 76.70% | 23.30% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0132053221 | GAT -> G | LOC_Os01g55630.1 | frameshift_variant ; p.Ile29fs; HIGH | frameshift_variant | Average:45.083; most accessible tissue: Callus, score: 69.065 | N | N | N | N |
| vg0132053221 | GAT -> GATAT | LOC_Os01g55630.1 | frameshift_variant&stop_gained ; p.Thr30fs; HIGH | frameshift_variant | Average:45.083; most accessible tissue: Callus, score: 69.065 | N | N | N | N |