| Variant ID: vg0627801112 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr06 | Position: 27801112 |
| Reference Allele: G | Alternative Allele: GAT |
| Primary Allele: G | Secondary Allele: GAT |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 300. )
TCTCAATGATATACAGGCCGGATGGGTGGTAAGTGAACAACTAACCTTAATTGTCTATGTTAACATTTGGAGGATGTGTAGTACAATCAACATCAGCTAT[G/GAT]
ATATATATATCTCATCTCAAATGCTATTTTCCCTACATATATAGATTGATCCAACCACCTATGGTGACAGCAAAACCCACTTCTTTGTATCTTGGACGGT
ACCGTCCAAGATACAAAGAAGTGGGTTTTGCTGTCACCATAGGTGGTTGGATCAATCTATATATGTAGGGAAAATAGCATTTGAGATGAGATATATATAT[C/ATC]
ATAGCTGATGTTGATTGTACTACACATCCTCCAAATGTTAACATAGACAATTAAGGTTAGTTGTTCACTTACCACCCATCCGGCCTGTATATCATTGAGA
| Populations | Population Size | Frequency of G(primary allele) | Frequency of GAT(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.10% | 0.80% | 0.11% | 0.00% | NA |
| All Indica | 2759 | 99.90% | 0.00% | 0.04% | 0.00% | NA |
| All Japonica | 1512 | 97.40% | 2.40% | 0.26% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.60% | 0.20% | 0.22% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 99.50% | 0.10% | 0.39% | 0.00% | NA |
| Tropical Japonica | 504 | 94.20% | 5.60% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 97.10% | 2.90% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 100.00% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0627801112 | G -> GAT | LOC_Os06g45910.1 | downstream_gene_variant ; 2533.0bp to feature; MODIFIER | silent_mutation | Average:47.297; most accessible tissue: Callus, score: 67.738 | N | N | N | N |
| vg0627801112 | G -> GAT | LOC_Os06g45920.1 | intron_variant ; MODIFIER | silent_mutation | Average:47.297; most accessible tissue: Callus, score: 67.738 | N | N | N | N |