| Variant ID: vg0724211173 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr07 | Position: 24211173 |
| Reference Allele: G | Alternative Allele: GTGT |
| Primary Allele: G | Secondary Allele: GTGT |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 259. )
TCTCTCCTCCGGGTAGAGCTAGATGCACCTGCTTTGCTCGCGCTGTGGTTACATGTGCCACGTTTCTCGTGTTCTTGATCGCTTCTCTGATCTTTCTCTC[G/GTGT]
TGTTTTTTTTTCTCTCTTTTTTTTTCATTTCTCTTCGCGCGCGGAAACTGTTTCTTGTTACTCTTTTGATCCGGTCGCGTTTTTCTCTTTCACTTTTTAT
ATAAAAAGTGAAAGAGAAAAACGCGACCGGATCAAAAGAGTAACAAGAAACAGTTTCCGCGCGCGAAGAGAAATGAAAAAAAAAGAGAGAAAAAAAAACA[C/ACAC]
GAGAGAAAGATCAGAGAAGCGATCAAGAACACGAGAAACGTGGCACATGTAACCACAGCGCGAGCAAAGCAGGTGCATCTAGCTCTACCCGGAGGAGAGA
| Populations | Population Size | Frequency of G(primary allele) | Frequency of GTGT(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 82.00% | 3.20% | 10.98% | 3.81% | NA |
| All Indica | 2759 | 89.60% | 5.40% | 4.57% | 0.51% | NA |
| All Japonica | 1512 | 65.80% | 0.00% | 23.88% | 10.32% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.30% | 0.00% | 0.34% | 0.34% | NA |
| Indica II | 465 | 84.10% | 7.10% | 7.31% | 1.51% | NA |
| Indica III | 913 | 83.40% | 10.50% | 6.02% | 0.11% | NA |
| Indica Intermediate | 786 | 92.60% | 2.40% | 4.45% | 0.51% | NA |
| Temperate Japonica | 767 | 89.00% | 0.00% | 10.04% | 0.91% | NA |
| Tropical Japonica | 504 | 37.50% | 0.00% | 39.68% | 22.82% | NA |
| Japonica Intermediate | 241 | 51.00% | 0.00% | 34.85% | 14.11% | NA |
| VI/Aromatic | 96 | 78.10% | 0.00% | 17.71% | 4.17% | NA |
| Intermediate | 90 | 74.40% | 2.20% | 16.67% | 6.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0724211173 | G -> DEL | N | N | silent_mutation | Average:63.756; most accessible tissue: Callus, score: 88.369 | N | N | N | N |
| vg0724211173 | G -> GTGT | LOC_Os07g40370.1 | upstream_gene_variant ; 3209.0bp to feature; MODIFIER | silent_mutation | Average:63.756; most accessible tissue: Callus, score: 88.369 | N | N | N | N |
| vg0724211173 | G -> GTGT | LOC_Os07g40390.1 | downstream_gene_variant ; 4704.0bp to feature; MODIFIER | silent_mutation | Average:63.756; most accessible tissue: Callus, score: 88.369 | N | N | N | N |
| vg0724211173 | G -> GTGT | LOC_Os07g40380.1 | intron_variant ; MODIFIER | silent_mutation | Average:63.756; most accessible tissue: Callus, score: 88.369 | N | N | N | N |