| Variant ID: vg0409085094 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr04 | Position: 9085094 |
| Reference Allele: G | Alternative Allele: GAT |
| Primary Allele: G | Secondary Allele: GAT |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 88. )
TTGGGATAGATCGGTCGCCATGCCGAGACAGTATAAATCACTTAGATCGAAATATATATTAATAATTAGACTATATACGTTCATAGCATAGCCGATCACG[G/GAT]
AGCTCTCCTATGGCGATCCTTGCCACCTCCTGACATGCATGGATGTAGTTTCTTCCTCCAGCTTCAAACATCACTGAGGGGATATCTTCACTATTACTGT
ACAGTAATAGTGAAGATATCCCCTCAGTGATGTTTGAAGCTGGAGGAAGAAACTACATCCATGCATGTCAGGAGGTGGCAAGGATCGCCATAGGAGAGCT[C/ATC]
CGTGATCGGCTATGCTATGAACGTATATAGTCTAATTATTAATATATATTTCGATCTAAGTGATTTATACTGTCTCGGCATGGCGACCGATCTATCCCAA
| Populations | Population Size | Frequency of G(primary allele) | Frequency of GAT(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 20.40% | 4.80% | 1.69% | 73.19% | NA |
| All Indica | 2759 | 0.80% | 5.40% | 0.43% | 93.33% | NA |
| All Japonica | 1512 | 60.80% | 3.00% | 2.65% | 33.53% | NA |
| Aus | 269 | 0.00% | 6.70% | 0.00% | 93.31% | NA |
| Indica I | 595 | 0.30% | 3.50% | 0.34% | 95.80% | NA |
| Indica II | 465 | 1.30% | 5.40% | 0.22% | 93.12% | NA |
| Indica III | 913 | 0.30% | 8.00% | 0.77% | 90.91% | NA |
| Indica Intermediate | 786 | 1.40% | 3.90% | 0.25% | 94.40% | NA |
| Temperate Japonica | 767 | 95.80% | 0.00% | 0.13% | 4.04% | NA |
| Tropical Japonica | 504 | 4.20% | 7.70% | 6.35% | 81.75% | NA |
| Japonica Intermediate | 241 | 68.00% | 2.50% | 2.90% | 26.56% | NA |
| VI/Aromatic | 96 | 0.00% | 7.30% | 22.92% | 69.79% | NA |
| Intermediate | 90 | 22.20% | 5.60% | 6.67% | 65.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0409085094 | G -> GAT | LOC_Os04g16700.1 | frameshift_variant ; p.Arg87fs; HIGH | frameshift_variant | Average:15.975; most accessible tissue: Minghui63 panicle, score: 25.313 | N | N | N | N |
| vg0409085094 | G -> DEL | LOC_Os04g16700.1 | N | frameshift_variant | Average:15.975; most accessible tissue: Minghui63 panicle, score: 25.313 | N | N | N | N |