| Variant ID: vg0101920424 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr01 | Position: 1920424 |
| Reference Allele: C | Alternative Allele: CAT |
| Primary Allele: C | Secondary Allele: CAT |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 304. )
AGCCATAGACAAGAGTACCGACCCAATCCCACCTACGGCCGGAACCCCCGGGACAGGCAGGCAGGACTGAGCCCCTAGCAGCAGGACACCGGCCCTGTGC[C/CAT]
ATGACATCTCGACTACCGGGCCGCAGCTCGTGTAGCCTTCATTTGCCCTGGAGAATGTCCATCGACCCCCGACTTCATCCATCTCCATCCGTGTACTTTT
AAAAGTACACGGATGGAGATGGATGAAGTCGGGGGTCGATGGACATTCTCCAGGGCAAATGAAGGCTACACGAGCTGCGGCCCGGTAGTCGAGATGTCAT[G/ATG]
GCACAGGGCCGGTGTCCTGCTGCTAGGGGCTCAGTCCTGCCTGCCTGTCCCGGGGGTTCCGGCCGTAGGTGGGATTGGGTCGGTACTCTTGTCTATGGCT
| Populations | Population Size | Frequency of C(primary allele) | Frequency of CAT(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 88.90% | 0.80% | 2.22% | 8.13% | NA |
| All Indica | 2759 | 91.40% | 1.20% | 3.19% | 4.13% | NA |
| All Japonica | 1512 | 81.40% | 0.10% | 0.86% | 17.59% | NA |
| Aus | 269 | 99.60% | 0.00% | 0.00% | 0.37% | NA |
| Indica I | 595 | 82.40% | 0.30% | 5.21% | 12.10% | NA |
| Indica II | 465 | 93.30% | 0.00% | 3.66% | 3.01% | NA |
| Indica III | 913 | 94.90% | 2.70% | 2.30% | 0.11% | NA |
| Indica Intermediate | 786 | 93.30% | 0.90% | 2.42% | 3.44% | NA |
| Temperate Japonica | 767 | 88.90% | 0.00% | 0.39% | 10.69% | NA |
| Tropical Japonica | 504 | 78.40% | 0.20% | 1.19% | 20.24% | NA |
| Japonica Intermediate | 241 | 63.90% | 0.40% | 1.66% | 34.02% | NA |
| VI/Aromatic | 96 | 99.00% | 0.00% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 93.30% | 0.00% | 3.33% | 3.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0101920424 | C -> CAT | LOC_Os01g04310.1 | frameshift_variant ; p.Trp3fs; HIGH | frameshift_variant | Average:6.858; most accessible tissue: Zhenshan97 flag leaf, score: 10.769 | N | N | N | N |
| vg0101920424 | C -> DEL | LOC_Os01g04310.1 | N | frameshift_variant | Average:6.858; most accessible tissue: Zhenshan97 flag leaf, score: 10.769 | N | N | N | N |