| Variant ID: vg0801634736 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr08 | Position: 1634736 |
| Reference Allele: CAA | Alternative Allele: C |
| Primary Allele: CAA | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
TCCGGTCCTCCGCCTTCGCCGCCTGCGGCTACAGGTGGTCCGTCCGCGTCTACCCCGGCGGGTTCGGGCCGGCGCACCGGGAGTTCGTGTCGGTGTTCGT[CAA/C]
GATGATGACCAACAGGGGCAAGGCGGCGGCGCGGTTCGACCTCCGGCTGATCGACCGCGCCACCGGGCTGCCCCGCTCGGTGTTCCGGGCGGCGCAGCCA
TGGCTGCGCCGCCCGGAACACCGAGCGGGGCAGCCCGGTGGCGCGGTCGATCAGCCGGAGGTCGAACCGCGCCGCCGCCTTGCCCCTGTTGGTCATCATC[TTG/G]
ACGAACACCGACACGAACTCCCGGTGCGCCGGCCCGAACCCGCCGGGGTAGACGCGGACGGACCACCTGTAGCCGCAGGCGGCGAAGGCGGAGGACCGGA
| Populations | Population Size | Frequency of CAA(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 86.00% | 13.30% | 0.02% | 0.74% | NA |
| All Indica | 2759 | 98.60% | 0.10% | 0.04% | 1.27% | NA |
| All Japonica | 1512 | 59.90% | 40.10% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 97.50% | 0.00% | 0.00% | 2.52% | NA |
| Indica II | 465 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.30% | 0.00% | 0.00% | 0.66% | NA |
| Indica Intermediate | 786 | 97.70% | 0.40% | 0.13% | 1.78% | NA |
| Temperate Japonica | 767 | 96.30% | 3.70% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 16.10% | 83.90% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 35.30% | 64.70% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 97.90% | 2.10% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 83.30% | 16.70% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0801634736 | CAA -> C | LOC_Os08g03490.1 | frameshift_variant ; p.Lys79fs; HIGH | frameshift_variant | Average:76.955; most accessible tissue: Minghui63 flag leaf, score: 82.053 | N | N | N | N |
| vg0801634736 | CAA -> DEL | LOC_Os08g03490.1 | N | frameshift_variant | Average:76.955; most accessible tissue: Minghui63 flag leaf, score: 82.053 | N | N | N | N |