| Variant ID: vg0121065693 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr01 | Position: 21065693 |
| Reference Allele: C | Alternative Allele: CTGA |
| Primary Allele: C | Secondary Allele: CTGA |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 318. )
CAAGAGTCTCAGGAGATGGTGACACCGGTCGAGATGCAATCTCAAGATGAGGGAGGTGAAATGACAAATGAGAAGCTATTAATGCATGAATGTTCCCCAA[C/CTGA]
TGATGATGATTTTGAGAGATGTCAGATTCCCACTGATTCTGACATTGAAAGACTTAGAGAGGAAGAAGATAATGAAGAGGACAATTTCCAAGAGGTGTCT
AGACACCTCTTGGAAATTGTCCTCTTCATTATCTTCTTCCTCTCTAAGTCTTTCAATGTCAGAATCAGTGGGAATCTGACATCTCTCAAAATCATCATCA[G/TCAG]
TTGGGGAACATTCATGCATTAATAGCTTCTCATTTGTCATTTCACCTCCCTCATCTTGAGATTGCATCTCGACCGGTGTCACCATCTCCTGAGACTCTTG
| Populations | Population Size | Frequency of C(primary allele) | Frequency of CTGA(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 97.60% | 0.20% | 0.21% | 1.99% | NA |
| All Indica | 2759 | 99.60% | 0.30% | 0.04% | 0.00% | NA |
| All Japonica | 1512 | 93.30% | 0.00% | 0.60% | 6.08% | NA |
| Aus | 269 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.60% | 0.20% | 0.22% | 0.00% | NA |
| Indica III | 913 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.50% | 0.50% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 99.60% | 0.00% | 0.00% | 0.39% | NA |
| Tropical Japonica | 504 | 95.60% | 0.00% | 0.40% | 3.97% | NA |
| Japonica Intermediate | 241 | 68.50% | 0.00% | 2.90% | 28.63% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 97.80% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0121065693 | C -> CTGA | LOC_Os01g37660.1 | inframe_insertion ; p.Asp81dup; MODERATE | inframe_variant | Average:45.887; most accessible tissue: Zhenshan97 flag leaf, score: 74.162 | N | N | N | N |
| vg0121065693 | C -> DEL | LOC_Os01g37660.1 | N | frameshift_variant | Average:45.887; most accessible tissue: Zhenshan97 flag leaf, score: 74.162 | N | N | N | N |