| Variant ID: vg0128509373 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr01 | Position: 28509373 |
| Reference Allele: ATATAT | Alternative Allele: AGAGATGGTATAT,A |
| Primary Allele: ATATAT | Secondary Allele: AGAGATGGTATAT |
Inferred Ancestral Allele: Not determined.
TACTGAGATCACGGTTTCGTAGGAAGCGGTTCGCGCCGTTTTTCCCACGACACGCTCCTGTCAGGTGCCGTTGTACGGCGGTGCCAGATTGGGGTGTGAC[ATATAT/AGAGATGGTATAT,A]
GAACGATGGGAGGCGCGTGATGGTGGCGGTGTCTAGGCCGAACCTGGGCAGCGTCGGCTGCTGCTGCTCCTGCTCCATGACCAGTGGACGATCACGCCGG
CCGGCGTGATCGTCCACTGGTCATGGAGCAGGAGCAGCAGCAGCCGACGCTGCCCAGGTTCGGCCTAGACACCGCCACCATCACGCGCCTCCCATCGTTC[ATATAT/ATATACCATCTCT,T]
GTCACACCCCAATCTGGCACCGCCGTACAACGGCACCTGACAGGAGCGTGTCGTGGGAAAAACGGCGCGAACCGCTTCCTACGAAACCGTGATCTCAGTA
| Populations | Population Size | Frequency of ATATAT(primary allele) | Frequency of AGAGATGGTATAT(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 25.20% | 0.10% | 4.34% | 70.17% | A: 0.11% |
| All Indica | 2759 | 1.40% | 0.30% | 5.29% | 92.82% | A: 0.18% |
| All Japonica | 1512 | 72.60% | 0.00% | 3.44% | 23.94% | NA |
| Aus | 269 | 4.10% | 0.00% | 1.12% | 94.80% | NA |
| Indica I | 595 | 1.70% | 0.30% | 3.03% | 94.96% | NA |
| Indica II | 465 | 2.60% | 0.00% | 0.00% | 97.42% | NA |
| Indica III | 913 | 0.70% | 0.20% | 12.60% | 86.09% | A: 0.44% |
| Indica Intermediate | 786 | 1.50% | 0.40% | 1.65% | 96.31% | A: 0.13% |
| Temperate Japonica | 767 | 92.80% | 0.00% | 6.52% | 0.65% | NA |
| Tropical Japonica | 504 | 34.10% | 0.00% | 0.40% | 65.48% | NA |
| Japonica Intermediate | 241 | 88.80% | 0.00% | 0.00% | 11.20% | NA |
| VI/Aromatic | 96 | 14.60% | 0.00% | 1.04% | 84.38% | NA |
| Intermediate | 90 | 33.30% | 0.00% | 3.33% | 63.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0128509373 | ATATAT -> A | LOC_Os01g49570.1 | frameshift_variant ; p.Ile66fs; HIGH | frameshift_variant | Average:21.498; most accessible tissue: Zhenshan97 panicle, score: 39.652 | N | N | N | N |
| vg0128509373 | ATATAT -> DEL | LOC_Os01g49570.1 | N | frameshift_variant | Average:21.498; most accessible tissue: Zhenshan97 panicle, score: 39.652 | N | N | N | N |
| vg0128509373 | ATATAT -> AGAGATGGTATAT | LOC_Os01g49570.1 | frameshift_variant ; p.Val68fs; HIGH | frameshift_variant | Average:21.498; most accessible tissue: Zhenshan97 panicle, score: 39.652 | N | N | N | N |