| Variant ID: vg0100791529 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr01 | Position: 791529 |
| Reference Allele: A | Alternative Allele: ACAT |
| Primary Allele: A | Secondary Allele: ACAT |
Inferred Ancestral Allele: Not determined.
TACATTTGAAGGTCGAAATGTTTCTCAAGACATATGGCACATCGAAACCCACAAGGTATAGTTTCTCTGAAGTTAAGAAGATTACAAGACGGTTCAGGGA[A/ACAT]
AAGATAGGCCACGGTGGGTATGGAAATGTATACAAGGGTGAGCTACCAAATGGAGTGCCCGTGGCAGTTAAGATGCTAGAAAATTCCAGAGGCGACGGGC
GCCCGTCGCCTCTGGAATTTTCTAGCATCTTAACTGCCACGGGCACTCCATTTGGTAGCTCACCCTTGTATACATTTCCATACCCACCGTGGCCTATCTT[T/ATGT]
TCCCTGAACCGTCTTGTAATCTTCTTAACTTCAGAGAAACTATACCTTGTGGGTTTCGATGTGCCATATGTCTTGAGAAACATTTCGACCTTCAAATGTA
| Populations | Population Size | Frequency of A(primary allele) | Frequency of ACAT(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 55.90% | 1.40% | 1.82% | 40.86% | NA |
| All Indica | 2759 | 49.80% | 1.20% | 2.54% | 46.47% | NA |
| All Japonica | 1512 | 72.50% | 1.10% | 0.46% | 25.93% | NA |
| Aus | 269 | 36.40% | 5.20% | 1.49% | 56.88% | NA |
| Indica I | 595 | 68.90% | 0.50% | 0.67% | 29.92% | NA |
| Indica II | 465 | 75.90% | 0.00% | 1.08% | 23.01% | NA |
| Indica III | 913 | 17.90% | 2.70% | 3.50% | 75.90% | NA |
| Indica Intermediate | 786 | 57.00% | 0.60% | 3.69% | 38.68% | NA |
| Temperate Japonica | 767 | 69.60% | 1.40% | 0.52% | 28.42% | NA |
| Tropical Japonica | 504 | 82.90% | 0.40% | 0.20% | 16.47% | NA |
| Japonica Intermediate | 241 | 59.80% | 1.70% | 0.83% | 37.76% | NA |
| VI/Aromatic | 96 | 10.40% | 2.10% | 3.12% | 84.38% | NA |
| Intermediate | 90 | 71.10% | 1.10% | 2.22% | 25.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0100791529 | A -> ACAT | LOC_Os01g02440.1 | inframe_insertion ; p.Glu268_Lys269insHis; MODERATE | inframe_variant | Average:54.257; most accessible tissue: Zhenshan97 panicle, score: 68.538 | N | N | N | N |
| vg0100791529 | A -> DEL | LOC_Os01g02440.1 | N | frameshift_variant | Average:54.257; most accessible tissue: Zhenshan97 panicle, score: 68.538 | N | N | N | N |