| Variant ID: vg1222420039 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr12 | Position: 22420039 |
| Reference Allele: GA | Alternative Allele: G,AA |
| Primary Allele: GA | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
GTCTCGCAGTTTATATGCGGAATTTATAATTTGTTTTGTTATTAGTCTACATTTAATACTTTAAATATGTTTCTGTATACTTAAAAAAGATTTGGCACAC[GA/G,AA]
ACTAAACACAGCCTAAATAAAGTGCTCAAGAATATACATGAGATTATATTCACAACATTGCCCATTCAGGTAGCCATCGAAGAAGAGGTAGCGGATACGT
ACGTATCCGCTACCTCTTCTTCGATGGCTACCTGAATGGGCAATGTTGTGAATATAATCTCATGTATATTCTTGAGCACTTTATTTAGGCTGTGTTTAGT[TC/C,TT]
GTGTGCCAAATCTTTTTTAAGTATACAGAAACATATTTAAAGTATTAAATGTAGACTAATAACAAAACAAATTATAAATTCCGCATATAAACTGCGAGAC
| Populations | Population Size | Frequency of GA(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 42.30% | 13.50% | 1.78% | 42.07% | AA: 0.40% |
| All Indica | 2759 | 32.10% | 6.40% | 2.61% | 58.25% | AA: 0.69% |
| All Japonica | 1512 | 68.30% | 18.50% | 0.60% | 12.63% | NA |
| Aus | 269 | 6.30% | 30.50% | 0.37% | 62.83% | NA |
| Indica I | 595 | 32.60% | 8.20% | 3.03% | 55.97% | AA: 0.17% |
| Indica II | 465 | 21.70% | 0.00% | 3.01% | 75.27% | NA |
| Indica III | 913 | 36.80% | 8.00% | 0.99% | 53.67% | AA: 0.55% |
| Indica Intermediate | 786 | 32.30% | 6.90% | 3.94% | 55.22% | AA: 1.65% |
| Temperate Japonica | 767 | 77.30% | 14.10% | 0.26% | 8.34% | NA |
| Tropical Japonica | 504 | 66.50% | 11.90% | 1.19% | 20.44% | NA |
| Japonica Intermediate | 241 | 43.20% | 46.50% | 0.41% | 9.96% | NA |
| VI/Aromatic | 96 | 9.40% | 85.40% | 1.04% | 4.17% | NA |
| Intermediate | 90 | 60.00% | 20.00% | 1.11% | 18.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1222420039 | GA -> DEL | N | N | silent_mutation | Average:11.24; most accessible tissue: Callus, score: 63.722 | N | N | N | N |
| vg1222420039 | GA -> G | LOC_Os12g36600.1 | downstream_gene_variant ; 4424.0bp to feature; MODIFIER | silent_mutation | Average:11.24; most accessible tissue: Callus, score: 63.722 | N | N | N | N |
| vg1222420039 | GA -> G | LOC_Os12g36610.1 | downstream_gene_variant ; 775.0bp to feature; MODIFIER | silent_mutation | Average:11.24; most accessible tissue: Callus, score: 63.722 | N | N | N | N |
| vg1222420039 | GA -> G | LOC_Os12g36620.1 | intron_variant ; MODIFIER | silent_mutation | Average:11.24; most accessible tissue: Callus, score: 63.722 | N | N | N | N |
| vg1222420039 | GA -> AA | LOC_Os12g36600.1 | downstream_gene_variant ; 4423.0bp to feature; MODIFIER | silent_mutation | Average:11.24; most accessible tissue: Callus, score: 63.722 | N | N | N | N |
| vg1222420039 | GA -> AA | LOC_Os12g36610.1 | downstream_gene_variant ; 774.0bp to feature; MODIFIER | silent_mutation | Average:11.24; most accessible tissue: Callus, score: 63.722 | N | N | N | N |
| vg1222420039 | GA -> AA | LOC_Os12g36620.1 | intron_variant ; MODIFIER | silent_mutation | Average:11.24; most accessible tissue: Callus, score: 63.722 | N | N | N | N |