| Variant ID: vg1222420007 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr12 | Position: 22420007 |
| Reference Allele: GTT | Alternative Allele: G |
| Primary Allele: GTT | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
CTAATGACAGATTAATTAGGCTTAATAGATTCGTCTCGCAGTTTATATGCGGAATTTATAATTTGTTTTGTTATTAGTCTACATTTAATACTTTAAATAT[GTT/G]
TCTGTATACTTAAAAAAGATTTGGCACACGAACTAAACACAGCCTAAATAAAGTGCTCAAGAATATACATGAGATTATATTCACAACATTGCCCATTCAG
CTGAATGGGCAATGTTGTGAATATAATCTCATGTATATTCTTGAGCACTTTATTTAGGCTGTGTTTAGTTCGTGTGCCAAATCTTTTTTAAGTATACAGA[AAC/C]
ATATTTAAAGTATTAAATGTAGACTAATAACAAAACAAATTATAAATTCCGCATATAAACTGCGAGACGAATCTATTAAGCCTAATTAATCTGTCATTAG
| Populations | Population Size | Frequency of GTT(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 42.90% | 12.90% | 0.66% | 43.53% | NA |
| All Indica | 2759 | 17.20% | 21.60% | 0.80% | 60.46% | NA |
| All Japonica | 1512 | 86.20% | 0.40% | 0.26% | 13.10% | NA |
| Aus | 269 | 34.60% | 0.70% | 1.12% | 63.57% | NA |
| Indica I | 595 | 23.90% | 16.80% | 0.67% | 58.66% | NA |
| Indica II | 465 | 5.80% | 15.70% | 1.08% | 77.42% | NA |
| Indica III | 913 | 15.90% | 29.00% | 0.66% | 54.44% | NA |
| Indica Intermediate | 786 | 20.40% | 20.00% | 0.89% | 58.78% | NA |
| Temperate Japonica | 767 | 91.10% | 0.00% | 0.39% | 8.47% | NA |
| Tropical Japonica | 504 | 77.20% | 1.20% | 0.00% | 21.63% | NA |
| Japonica Intermediate | 241 | 89.60% | 0.00% | 0.41% | 9.96% | NA |
| VI/Aromatic | 96 | 95.80% | 0.00% | 0.00% | 4.17% | NA |
| Intermediate | 90 | 71.10% | 8.90% | 2.22% | 17.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1222420007 | GTT -> DEL | N | N | silent_mutation | Average:11.11; most accessible tissue: Callus, score: 63.722 | N | N | N | N |
| vg1222420007 | GTT -> G | LOC_Os12g36600.1 | downstream_gene_variant ; 4392.0bp to feature; MODIFIER | silent_mutation | Average:11.11; most accessible tissue: Callus, score: 63.722 | N | N | N | N |
| vg1222420007 | GTT -> G | LOC_Os12g36610.1 | downstream_gene_variant ; 743.0bp to feature; MODIFIER | silent_mutation | Average:11.11; most accessible tissue: Callus, score: 63.722 | N | N | N | N |
| vg1222420007 | GTT -> G | LOC_Os12g36620.1 | intron_variant ; MODIFIER | silent_mutation | Average:11.11; most accessible tissue: Callus, score: 63.722 | N | N | N | N |