| Variant ID: vg0804462937 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr08 | Position: 4462937 |
| Reference Allele: GAGGCAACT | Alternative Allele: G |
| Primary Allele: GAGGCAACT | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
CTGTGTCCCGGAACCCTGACATAAAGAAGATATTAAGAGACATGCTGAAAGAAGTGAACAGTCTTGACAACACACAACCATGGTCTCCTAATGATGATGA[GAGGCAACT/G]
AGTCAATAAACTTAGAGATACACTCCAAGATAAAAGGTATGCAAACAGCCATGGCATTTTACATGCATGATTGTGGAATTAAAATTCGTATTTGATCCTA
TAGGATCAAATACGAATTTTAATTCCACAATCATGCATGTAAAATGCCATGGCTGTTTGCATACCTTTTATCTTGGAGTGTATCTCTAAGTTTATTGACT[AGTTGCCTC/C]
TCATCATCATTAGGAGACCATGGTTGTGTGTTGTCAAGACTGTTCACTTCTTTCAGCATGTCTCTTAATATCTTCTTTATGTCAGGGTTCCGGGACACAG
| Populations | Population Size | Frequency of GAGGCAACT(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 34.80% | 0.30% | 1.31% | 63.63% | NA |
| All Indica | 2759 | 5.20% | 0.50% | 0.98% | 93.29% | NA |
| All Japonica | 1512 | 95.00% | 0.00% | 0.13% | 4.89% | NA |
| Aus | 269 | 4.10% | 0.00% | 7.81% | 88.10% | NA |
| Indica I | 595 | 9.10% | 0.00% | 1.18% | 89.75% | NA |
| Indica II | 465 | 8.20% | 0.20% | 0.86% | 90.75% | NA |
| Indica III | 913 | 1.00% | 0.80% | 0.66% | 97.59% | NA |
| Indica Intermediate | 786 | 5.50% | 0.80% | 1.27% | 92.49% | NA |
| Temperate Japonica | 767 | 98.30% | 0.00% | 0.13% | 1.56% | NA |
| Tropical Japonica | 504 | 88.70% | 0.00% | 0.20% | 11.11% | NA |
| Japonica Intermediate | 241 | 97.50% | 0.00% | 0.00% | 2.49% | NA |
| VI/Aromatic | 96 | 14.60% | 0.00% | 9.38% | 76.04% | NA |
| Intermediate | 90 | 42.20% | 0.00% | 3.33% | 54.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0804462937 | GAGGCAACT -> G | LOC_Os08g07920.1 | frameshift_variant ; p.Arg264fs; HIGH | frameshift_variant | Average:13.183; most accessible tissue: Callus, score: 80.37 | N | N | N | N |
| vg0804462937 | GAGGCAACT -> DEL | LOC_Os08g07920.1 | N | frameshift_variant | Average:13.183; most accessible tissue: Callus, score: 80.37 | N | N | N | N |