| Variant ID: vg1115080008 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr11 | Position: 15080008 |
| Reference Allele: G | Alternative Allele: GT |
| Primary Allele: G | Secondary Allele: GT |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 222. )
TCTGGTCAGCCTACAGAGACAAGTTCTGGCAAGGTGAGTTTATGTTCACACAGTTTCTCCATTTTCCTTAAGATCATAAAGTGCCAACCATATTTTCCTT[G/GT]
TTTTTTTTTCATTAAATGGGTGGTTTGATACTATTAGTAATATTGTATAGTGATAAGCAGGAAGCATGTCAGTAGATAGGAGTTGGATGCGCATGAGTAG
CTACTCATGCGCATCCAACTCCTATCTACTGACATGCTTCCTGCTTATCACTATACAATATTACTAATAGTATCAAACCACCCATTTAATGAAAAAAAAA[C/AC]
AAGGAAAATATGGTTGGCACTTTATGATCTTAAGGAAAATGGAGAAACTGTGTGAACATAAACTCACCTTGCCAGAACTTGTCTCTGTAGGCTGACCAGA
| Populations | Population Size | Frequency of G(primary allele) | Frequency of GT(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 47.70% | 0.20% | 27.95% | 24.23% | NA |
| All Indica | 2759 | 28.60% | 0.20% | 42.01% | 29.18% | NA |
| All Japonica | 1512 | 72.10% | 0.00% | 8.47% | 19.44% | NA |
| Aus | 269 | 94.40% | 0.40% | 1.49% | 3.72% | NA |
| Indica I | 595 | 22.90% | 0.50% | 29.92% | 46.72% | NA |
| Indica II | 465 | 18.30% | 0.00% | 59.35% | 22.37% | NA |
| Indica III | 913 | 35.70% | 0.00% | 42.61% | 21.69% | NA |
| Indica Intermediate | 786 | 30.80% | 0.40% | 40.20% | 28.63% | NA |
| Temperate Japonica | 767 | 79.10% | 0.00% | 11.21% | 9.65% | NA |
| Tropical Japonica | 504 | 64.90% | 0.00% | 5.95% | 29.17% | NA |
| Japonica Intermediate | 241 | 64.70% | 0.00% | 4.98% | 30.29% | NA |
| VI/Aromatic | 96 | 75.00% | 0.00% | 6.25% | 18.75% | NA |
| Intermediate | 90 | 52.20% | 1.10% | 26.67% | 20.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1115080008 | G -> GT | LOC_Os11g26340.1 | downstream_gene_variant ; 4043.0bp to feature; MODIFIER | silent_mutation | Average:15.593; most accessible tissue: Minghui63 root, score: 25.504 | N | N | N | N |
| vg1115080008 | G -> GT | LOC_Os11g26360.1 | downstream_gene_variant ; 2821.0bp to feature; MODIFIER | silent_mutation | Average:15.593; most accessible tissue: Minghui63 root, score: 25.504 | N | N | N | N |
| vg1115080008 | G -> GT | LOC_Os11g26350.1 | intron_variant ; MODIFIER | silent_mutation | Average:15.593; most accessible tissue: Minghui63 root, score: 25.504 | N | N | N | N |
| vg1115080008 | G -> DEL | N | N | silent_mutation | Average:15.593; most accessible tissue: Minghui63 root, score: 25.504 | N | N | N | N |