| Variant ID: vg0410565217 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr04 | Position: 10565217 |
| Reference Allele: CAT | Alternative Allele: C |
| Primary Allele: CAT | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
ACAACAAATCTCTGCCAACCAACAACTTTCCAAATAGCACGAAAATCAACATCCATACCTATCTTTTTCAGCAGCTCCGGAGAGTATTCTCGTGTGTGAG[CAT/C]
ACTCCCGGTCACTCAGCATGTAGTAGGCTTGTCTTTCCCGATCGTCGACAAGGTCGAGGTCGGCGTCATTCAAGAGACGTCGTGGAGCTTCGGCATCCTC
GAGGATGCCGAAGCTCCACGACGTCTCTTGAATGACGCCGACCTCGACCTTGTCGACGATCGGGAAAGACAAGCCTACTACATGCTGAGTGACCGGGAGT[ATG/G]
CTCACACACGAGAATACTCTCCGGAGCTGCTGAAAAAGATAGGTATGGATGTTGATTTTCGTGCTATTTGGAAAGTTGTTGGTTGGCAGAGATTTGTTGT
| Populations | Population Size | Frequency of CAT(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 29.80% | 0.10% | 6.16% | 63.92% | NA |
| All Indica | 2759 | 8.60% | 0.10% | 1.16% | 90.21% | NA |
| All Japonica | 1512 | 68.90% | 0.00% | 15.87% | 15.21% | NA |
| Aus | 269 | 5.20% | 0.00% | 0.74% | 94.05% | NA |
| Indica I | 595 | 5.00% | 0.00% | 1.01% | 93.95% | NA |
| Indica II | 465 | 25.40% | 0.00% | 1.29% | 73.33% | NA |
| Indica III | 913 | 2.30% | 0.00% | 0.77% | 96.93% | NA |
| Indica Intermediate | 786 | 8.50% | 0.30% | 1.65% | 89.57% | NA |
| Temperate Japonica | 767 | 96.90% | 0.00% | 1.83% | 1.30% | NA |
| Tropical Japonica | 504 | 23.20% | 0.00% | 38.89% | 37.90% | NA |
| Japonica Intermediate | 241 | 75.50% | 0.00% | 12.45% | 12.03% | NA |
| VI/Aromatic | 96 | 82.30% | 0.00% | 5.21% | 12.50% | NA |
| Intermediate | 90 | 43.30% | 2.20% | 13.33% | 41.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0410565217 | CAT -> C | LOC_Os04g19010.1 | frameshift_variant ; p.Tyr35fs; HIGH | frameshift_variant | Average:9.854; most accessible tissue: Callus, score: 40.877 | N | N | N | N |
| vg0410565217 | CAT -> DEL | LOC_Os04g19010.1 | N | frameshift_variant | Average:9.854; most accessible tissue: Callus, score: 40.877 | N | N | N | N |