| Variant ID: vg0128509380 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr01 | Position: 28509380 |
| Reference Allele: AAC | Alternative Allele: A |
| Primary Allele: AAC | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
ATCACGGTTTCGTAGGAAGCGGTTCGCGCCGTTTTTCCCACGACACGCTCCTGTCAGGTGCCGTTGTACGGCGGTGCCAGATTGGGGTGTGACATATATG[AAC/A]
GATGGGAGGCGCGTGATGGTGGCGGTGTCTAGGCCGAACCTGGGCAGCGTCGGCTGCTGCTGCTCCTGCTCCATGACCAGTGGACGATCACGCCGGCGAC
GTCGCCGGCGTGATCGTCCACTGGTCATGGAGCAGGAGCAGCAGCAGCCGACGCTGCCCAGGTTCGGCCTAGACACCGCCACCATCACGCGCCTCCCATC[GTT/T]
CATATATGTCACACCCCAATCTGGCACCGCCGTACAACGGCACCTGACAGGAGCGTGTCGTGGGAAAAACGGCGCGAACCGCTTCCTACGAAACCGTGAT
| Populations | Population Size | Frequency of AAC(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 40.80% | 0.10% | 9.31% | 49.83% | NA |
| All Indica | 2759 | 18.80% | 0.20% | 13.19% | 67.78% | NA |
| All Japonica | 1512 | 88.40% | 0.00% | 3.97% | 7.61% | NA |
| Aus | 269 | 4.10% | 0.00% | 2.23% | 93.68% | NA |
| Indica I | 595 | 6.90% | 0.00% | 8.40% | 84.71% | NA |
| Indica II | 465 | 9.70% | 0.00% | 11.40% | 78.92% | NA |
| Indica III | 913 | 35.60% | 0.40% | 18.62% | 45.35% | NA |
| Indica Intermediate | 786 | 13.90% | 0.10% | 11.58% | 74.43% | NA |
| Temperate Japonica | 767 | 92.80% | 0.00% | 6.78% | 0.39% | NA |
| Tropical Japonica | 504 | 78.20% | 0.00% | 1.39% | 20.44% | NA |
| Japonica Intermediate | 241 | 95.90% | 0.00% | 0.41% | 3.73% | NA |
| VI/Aromatic | 96 | 14.60% | 0.00% | 2.08% | 83.33% | NA |
| Intermediate | 90 | 48.90% | 0.00% | 8.89% | 42.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0128509380 | AAC -> A | LOC_Os01g49570.1 | frameshift_variant ; p.Phe65fs; HIGH | frameshift_variant | Average:21.355; most accessible tissue: Zhenshan97 panicle, score: 39.652 | N | N | N | N |
| vg0128509380 | AAC -> DEL | LOC_Os01g49570.1 | N | frameshift_variant | Average:21.355; most accessible tissue: Zhenshan97 panicle, score: 39.652 | N | N | N | N |