| Variant ID: vg0724211175 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr07 | Position: 24211175 |
| Reference Allele: GT | Alternative Allele: G |
| Primary Allele: GT | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
TCTCCTCCGGGTAGAGCTAGATGCACCTGCTTTGCTCGCGCTGTGGTTACATGTGCCACGTTTCTCGTGTTCTTGATCGCTTCTCTGATCTTTCTCTCGT[GT/G]
TTTTTTTTCTCTCTTTTTTTTTCATTTCTCTTCGCGCGCGGAAACTGTTTCTTGTTACTCTTTTGATCCGGTCGCGTTTTTCTCTTTCACTTTTTATTTC
GAAATAAAAAGTGAAAGAGAAAAACGCGACCGGATCAAAAGAGTAACAAGAAACAGTTTCCGCGCGCGAAGAGAAATGAAAAAAAAAGAGAGAAAAAAAA[AC/C]
ACGAGAGAAAGATCAGAGAAGCGATCAAGAACACGAGAAACGTGGCACATGTAACCACAGCGCGAGCAAAGCAGGTGCATCTAGCTCTACCCGGAGGAGA
| Populations | Population Size | Frequency of GT(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 75.30% | 24.60% | 0.02% | 0.00% | NA |
| All Indica | 2759 | 94.40% | 5.60% | 0.04% | 0.00% | NA |
| All Japonica | 1512 | 47.00% | 53.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 51.70% | 48.30% | 0.00% | 0.00% | NA |
| Indica I | 595 | 94.80% | 5.20% | 0.00% | 0.00% | NA |
| Indica II | 465 | 91.00% | 9.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 97.20% | 2.80% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 92.90% | 7.00% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 81.50% | 18.50% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 6.90% | 93.10% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 21.20% | 78.80% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 50.00% | 50.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 65.60% | 34.40% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0724211175 | GT -> G | LOC_Os07g40370.1 | upstream_gene_variant ; 3211.0bp to feature; MODIFIER | silent_mutation | Average:64.237; most accessible tissue: Callus, score: 93.754 | N | N | N | N |
| vg0724211175 | GT -> G | LOC_Os07g40390.1 | downstream_gene_variant ; 4702.0bp to feature; MODIFIER | silent_mutation | Average:64.237; most accessible tissue: Callus, score: 93.754 | N | N | N | N |
| vg0724211175 | GT -> G | LOC_Os07g40380.1 | intron_variant ; MODIFIER | silent_mutation | Average:64.237; most accessible tissue: Callus, score: 93.754 | N | N | N | N |