| Variant ID: vg0724211846 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr07 | Position: 24211846 |
| Reference Allele: CGCCACGTTCAT | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: CGCCACGTTCAT |
Inferred Ancestral Allele: Not determined.
TGGCGCTTATGATGTACTCGCTTCTCATCGGGAACAGCCTTAGCGGCCGGACGGCTACCCCACATGGATATGGGGCTCCACCCCCATCTCCAGCTGGGCT[CGCCACGTTCAT/C]
GGGGGTCAGCTTCATGTGCCTCTCATTCGTGACGGTGGGCATGGTTCACCTTGTGCTTGTTCTTCATCTTACGATGGTGAGGGGAGTCGGCGGTTTTCCA
TGGAAAACCGCCGACTCCCCTCACCATCGTAAGATGAAGAACAAGCACAAGGTGAACCATGCCCACCGTCACGAATGAGAGGCACATGAAGCTGACCCCC[ATGAACGTGGCG/G]
AGCCCAGCTGGAGATGGGGGTGGAGCCCCATATCCATGTGGGGTAGCCGTCCGGCCGCTAAGGCTGTTCCCGATGAGAAGCGAGTACATCATAAGCGCCA
| Populations | Population Size | Frequency of C(primary allele) | Frequency of CGCCACGTTCAT(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 58.00% | 41.80% | 0.13% | 0.04% | NA |
| All Indica | 2759 | 91.80% | 7.90% | 0.22% | 0.07% | NA |
| All Japonica | 1512 | 0.80% | 99.20% | 0.00% | 0.00% | NA |
| Aus | 269 | 44.60% | 55.40% | 0.00% | 0.00% | NA |
| Indica I | 595 | 93.10% | 6.60% | 0.00% | 0.34% | NA |
| Indica II | 465 | 87.70% | 12.00% | 0.22% | 0.00% | NA |
| Indica III | 913 | 97.30% | 2.60% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 86.80% | 12.70% | 0.51% | 0.00% | NA |
| Temperate Japonica | 767 | 0.70% | 99.30% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 0.40% | 99.60% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 2.10% | 97.90% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 44.80% | 55.20% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 40.00% | 60.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0724211846 | CGCCACGTTCAT -> DEL | LOC_Os07g40380.1 | N | frameshift_variant | Average:64.393; most accessible tissue: Callus, score: 87.58 | N | N | N | N |
| vg0724211846 | CGCCACGTTCAT -> C | LOC_Os07g40380.1 | frameshift_variant ; p.Ala70fs; HIGH | frameshift_variant | Average:64.393; most accessible tissue: Callus, score: 87.58 | N | N | N | N |