| Variant ID: vg1222419795 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr12 | Position: 22419795 |
| Reference Allele: TAC | Alternative Allele: T |
| Primary Allele: TAC | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
AAGACAAGACAATATACTAGAAATATCAACATTTTAGGCCAAGTTTAGTTCCAAAATTTTTCTTCAAACTTTCAACTTTTTCATCACATCAAAACTTTCC[TAC/T]
ACACACAAATTTCCAACTTTTCCGTCACATCATTCCAATTTTAACCAAATTTCTAATTTTGGCGTTGATTTGATATGATTTGACAATGTGATGCTACCGT
ACGGTAGCATCACATTGTCAAATCATATCAAATCAACGCCAAAATTAGAAATTTGGTTAAAATTGGAATGATGTGACGGAAAAGTTGGAAATTTGTGTGT[GTA/A]
GGAAAGTTTTGATGTGATGAAAAAGTTGAAAGTTTGAAGAAAAATTTTGGAACTAAACTTGGCCTAAAATGTTGATATTTCTAGTATATTGTCTTGTCTT
| Populations | Population Size | Frequency of TAC(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 43.00% | 13.50% | 1.14% | 42.34% | NA |
| All Indica | 2759 | 33.30% | 6.40% | 1.70% | 58.61% | NA |
| All Japonica | 1512 | 68.30% | 18.50% | 0.07% | 13.16% | NA |
| Aus | 269 | 7.10% | 30.50% | 2.23% | 60.22% | NA |
| Indica I | 595 | 34.50% | 8.10% | 1.85% | 55.63% | NA |
| Indica II | 465 | 22.60% | 0.00% | 1.72% | 75.70% | NA |
| Indica III | 913 | 37.00% | 8.30% | 1.10% | 53.56% | NA |
| Indica Intermediate | 786 | 34.50% | 6.60% | 2.29% | 56.62% | NA |
| Temperate Japonica | 767 | 77.30% | 14.10% | 0.13% | 8.47% | NA |
| Tropical Japonica | 504 | 66.50% | 11.90% | 0.00% | 21.63% | NA |
| Japonica Intermediate | 241 | 43.20% | 46.50% | 0.00% | 10.37% | NA |
| VI/Aromatic | 96 | 9.40% | 85.40% | 0.00% | 5.21% | NA |
| Intermediate | 90 | 58.90% | 21.10% | 0.00% | 20.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1222419795 | TAC -> DEL | LOC_Os12g36620.1 | N | splice_acceptor_variant | Average:9.666; most accessible tissue: Callus, score: 56.791 | N | N | N | N |
| vg1222419795 | TAC -> T | LOC_Os12g36620.1 | splice_region_variant&intron_variant ; LOW | silent_mutation | Average:9.666; most accessible tissue: Callus, score: 56.791 | N | N | N | N |
| vg1222419795 | TAC -> T | LOC_Os12g36600.1 | downstream_gene_variant ; 4180.0bp to feature; MODIFIER | silent_mutation | Average:9.666; most accessible tissue: Callus, score: 56.791 | N | N | N | N |
| vg1222419795 | TAC -> T | LOC_Os12g36610.1 | downstream_gene_variant ; 531.0bp to feature; MODIFIER | silent_mutation | Average:9.666; most accessible tissue: Callus, score: 56.791 | N | N | N | N |