| Variant ID: vg0108457638 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr01 | Position: 8457638 |
| Reference Allele: C | Alternative Allele: CA |
| Primary Allele: C | Secondary Allele: CA |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 241. )
GCTATTCCCCTACGGTGTCTCCGGATACCGTCAGGAGATACGAAAGCGCTATCTCTGATCTCGCCGGGCACAGATTCGAGGAGGAAGACTACCCTGTTGT[C/CA]
GACTACGAGTCAGACCTTCAGACCGACATGTCCACAACAGTTAGATAGGCTACCCACATATTGTACTGGTGTGATTATGGTGAATAAAAGCAATACCGGC
GCCGGTATTGCTTTTATTCACCATAATCACACCAGTACAATATGTGGGTAGCCTATCTAACTGTTGTGGACATGTCGGTCTGAAGGTCTGACTCGTAGTC[G/TG]
ACAACAGGGTAGTCTTCCTCCTCGAATCTGTGCCCGGCGAGATCAGAGATAGCGCTTTCGTATCTCCTGACGGTATCCGGAGACACCGTAGGGGAATAGC
| Populations | Population Size | Frequency of C(primary allele) | Frequency of CA(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 93.10% | 5.90% | 0.95% | 0.02% | NA |
| All Indica | 2759 | 96.40% | 2.90% | 0.65% | 0.04% | NA |
| All Japonica | 1512 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Aus | 269 | 18.60% | 71.70% | 9.67% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 98.10% | 1.90% | 0.00% | 0.00% | NA |
| Indica III | 913 | 95.30% | 3.70% | 0.99% | 0.00% | NA |
| Indica Intermediate | 786 | 94.00% | 4.70% | 1.15% | 0.13% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.40% | 0.60% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 96.70% | 2.20% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0108457638 | C -> DEL | LOC_Os01g15070.1 | N | frameshift_variant | Average:52.341; most accessible tissue: Zhenshan97 panicle, score: 69.946 | N | N | N | N |
| vg0108457638 | C -> CA | LOC_Os01g15070.1 | frameshift_variant ; p.Asp72fs; HIGH | frameshift_variant | Average:52.341; most accessible tissue: Zhenshan97 panicle, score: 69.946 | N | N | N | N |