| Variant ID: vg0234180290 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr02 | Position: 34180290 |
| Reference Allele: ATGGTGG | Alternative Allele: A |
| Primary Allele: ATGGTGG | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
AAGTTTCAGGGAGATCGCTTGCAAAGACCCCCACCTGTCCCTGCAGCAGGTAAGAAAAAATTACAGTGGAGCAGAATTTGGGGCGGTTCATCTTCTAGCC[ATGGTGG/A]
TGGTACCAGTTCATCAGCAGCAAGTGGGGACGCTAGATCGCATGGTCCTGCCGAAGAGTTGTCCAACTATTTGGATAGCGATGCCATCAGGCATGAAACG
CGTTTCATGCCTGATGGCATCGCTATCCAAATAGTTGGACAACTCTTCGGCAGGACCATGCGATCTAGCGTCCCCACTTGCTGCTGATGAACTGGTACCA[CCACCAT/T]
GGCTAGAAGATGAACCGCCCCAAATTCTGCTCCACTGTAATTTTTTCTTACCTGCTGCAGGGACAGGTGGGGGTCTTTGCAAGCGATCTCCCTGAAACTT
| Populations | Population Size | Frequency of ATGGTGG(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 45.10% | 0.70% | 2.54% | 51.61% | NA |
| All Indica | 2759 | 20.80% | 0.80% | 2.72% | 75.68% | NA |
| All Japonica | 1512 | 97.40% | 0.00% | 0.00% | 2.65% | NA |
| Aus | 269 | 2.60% | 4.80% | 14.13% | 78.44% | NA |
| Indica I | 595 | 18.20% | 0.30% | 1.18% | 80.34% | NA |
| Indica II | 465 | 12.00% | 0.20% | 2.15% | 85.59% | NA |
| Indica III | 913 | 26.60% | 1.60% | 5.26% | 66.48% | NA |
| Indica Intermediate | 786 | 21.40% | 0.40% | 1.27% | 76.97% | NA |
| Temperate Japonica | 767 | 97.10% | 0.00% | 0.00% | 2.87% | NA |
| Tropical Japonica | 504 | 99.20% | 0.00% | 0.00% | 0.79% | NA |
| Japonica Intermediate | 241 | 94.20% | 0.00% | 0.00% | 5.81% | NA |
| VI/Aromatic | 96 | 27.10% | 0.00% | 5.21% | 67.71% | NA |
| Intermediate | 90 | 57.80% | 1.10% | 2.22% | 38.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0234180290 | ATGGTGG -> A | LOC_Os02g55830.1 | inframe_deletion ; p.Gly426_Gly427del; MODERATE | inframe_variant | Average:9.274; most accessible tissue: Zhenshan97 root, score: 16.934 | N | N | N | N |
| vg0234180290 | ATGGTGG -> DEL | LOC_Os02g55830.1 | N | frameshift_variant | Average:9.274; most accessible tissue: Zhenshan97 root, score: 16.934 | N | N | N | N |