| Variant ID: vg0100791524 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr01 | Position: 791524 |
| Reference Allele: AGGG | Alternative Allele: A |
| Primary Allele: AGGG | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
AGAGATACATTTGAAGGTCGAAATGTTTCTCAAGACATATGGCACATCGAAACCCACAAGGTATAGTTTCTCTGAAGTTAAGAAGATTACAAGACGGTTC[AGGG/A]
AAAAGATAGGCCACGGTGGGTATGGAAATGTATACAAGGGTGAGCTACCAAATGGAGTGCCCGTGGCAGTTAAGATGCTAGAAAATTCCAGAGGCGACGG
CCGTCGCCTCTGGAATTTTCTAGCATCTTAACTGCCACGGGCACTCCATTTGGTAGCTCACCCTTGTATACATTTCCATACCCACCGTGGCCTATCTTTT[CCCT/T]
GAACCGTCTTGTAATCTTCTTAACTTCAGAGAAACTATACCTTGTGGGTTTCGATGTGCCATATGTCTTGAGAAACATTTCGACCTTCAAATGTATCTCT
| Populations | Population Size | Frequency of AGGG(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 91.30% | 1.10% | 2.69% | 4.91% | NA |
| All Indica | 2759 | 91.80% | 1.00% | 4.17% | 3.04% | NA |
| All Japonica | 1512 | 98.50% | 0.90% | 0.40% | 0.20% | NA |
| Aus | 269 | 53.20% | 3.00% | 1.12% | 42.75% | NA |
| Indica I | 595 | 94.80% | 0.20% | 4.54% | 0.50% | NA |
| Indica II | 465 | 95.50% | 0.00% | 3.44% | 1.08% | NA |
| Indica III | 913 | 89.70% | 2.50% | 3.94% | 3.83% | NA |
| Indica Intermediate | 786 | 89.70% | 0.50% | 4.58% | 5.22% | NA |
| Temperate Japonica | 767 | 98.00% | 1.20% | 0.52% | 0.26% | NA |
| Tropical Japonica | 504 | 99.20% | 0.40% | 0.40% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.30% | 1.20% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 74.00% | 0.00% | 2.08% | 23.96% | NA |
| Intermediate | 90 | 90.00% | 1.10% | 1.11% | 7.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0100791524 | AGGG -> A | LOC_Os01g02440.1 | disruptive_inframe_deletion ; p.Arg267_Glu268delinsLys; MODERATE | inframe_variant | Average:53.902; most accessible tissue: Zhenshan97 panicle, score: 68.538 | N | N | N | N |
| vg0100791524 | AGGG -> DEL | LOC_Os01g02440.1 | N | frameshift_variant | Average:53.902; most accessible tissue: Zhenshan97 panicle, score: 68.538 | N | N | N | N |