| Variant ID: vg0121065560 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr01 | Position: 21065560 |
| Reference Allele: TG | Alternative Allele: T |
| Primary Allele: TG | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GATGACTCATAGTGGGAAAACCCTGAAGAAATTGGCATCAAAGAAAGATTCATTGCTGAAGAAAGTAGAAAAGACAGAATGTTGTACTACTATGGTGCTC[TG/T]
GGGGAAGAAGGAGGAAAATCTAGTCATAGAACAAGAGTCTCAGGAGATGGTGACACCGGTCGAGATGCAATCTCAAGATGAGGGAGGTGAAATGACAAAT
ATTTGTCATTTCACCTCCCTCATCTTGAGATTGCATCTCGACCGGTGTCACCATCTCCTGAGACTCTTGTTCTATGACTAGATTTTCCTCCTTCTTCCCC[CA/A]
GAGCACCATAGTAGTACAACATTCTGTCTTTTCTACTTTCTTCAGCAATGAATCTTTCTTTGATGCCAATTTCTTCAGGGTTTTCCCACTATGAGTCATC
| Populations | Population Size | Frequency of TG(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 97.40% | 0.40% | 0.08% | 2.09% | NA |
| All Indica | 2759 | 99.50% | 0.50% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 93.30% | 0.00% | 0.26% | 6.42% | NA |
| Aus | 269 | 98.10% | 1.90% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 98.80% | 1.20% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 99.60% | 0.00% | 0.00% | 0.39% | NA |
| Tropical Japonica | 504 | 95.40% | 0.00% | 0.20% | 4.37% | NA |
| Japonica Intermediate | 241 | 68.90% | 0.00% | 1.24% | 29.88% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 96.70% | 1.10% | 0.00% | 2.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0121065560 | TG -> T | LOC_Os01g37660.1 | frameshift_variant ; p.Lys36fs; HIGH | frameshift_variant | Average:50.167; most accessible tissue: Zhenshan97 flag leaf, score: 79.006 | N | N | N | N |
| vg0121065560 | TG -> DEL | LOC_Os01g37660.1 | N | frameshift_variant | Average:50.167; most accessible tissue: Zhenshan97 flag leaf, score: 79.006 | N | N | N | N |