| Variant ID: vg1223515373 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr12 | Position: 23515373 |
| Reference Allele: CCATAAGACAAAAAAAAAGTTGT | Alternative Allele: C |
| Primary Allele: CCATAAGACAAAAAAAAAGT TGT | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
CTTTGATGATTTTGATGTACTTTCCATCATAGAAGAATACTATGTTAGCCCCAATAGTTCTGCTTACAATTGATTTGAAGTTATATTCAGTTGAAGCCAT[CCATAAGACAAAAAAAAAGTTGT/C]
CATTTCTAGTTACTGAATTTTGCGTTCTGTTTTTTGTTTTCTTGGTTCAGAAAGATGTACCCTGACCTGGCTGAGAAGATCACCACCACCACCACTACTG
CAGTAGTGGTGGTGGTGGTGATCTTCTCAGCCAGGTCAGGGTACATCTTTCTGAACCAAGAAAACAAAAAACAGAACGCAAAATTCAGTAACTAGAAATG[ACAACTTTTTTTTTGTCTTATGG/G]
ATGGCTTCAACTGAATATAACTTCAAATCAATTGTAAGCAGAACTATTGGGGCTAACATAGTATTCTTCTATGATGGAAAGTACATCAAAATCATCAAAG
| Populations | Population Size | Frequency of CCATAAGACAAAAAAAAAGT TGT(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.00% | 0.20% | 0.78% | 0.00% | NA |
| All Indica | 2759 | 98.40% | 0.30% | 1.23% | 0.00% | NA |
| All Japonica | 1512 | 99.90% | 0.00% | 0.13% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 98.50% | 0.00% | 1.51% | 0.00% | NA |
| Indica II | 465 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica III | 913 | 98.70% | 0.30% | 0.99% | 0.00% | NA |
| Indica Intermediate | 786 | 97.50% | 0.50% | 2.04% | 0.00% | NA |
| Temperate Japonica | 767 | 99.70% | 0.00% | 0.26% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 98.90% | 0.00% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1223515373 | CCATAAGACAAAAAAAAAGTTGT -> C | LOC_Os12g38310.1 | upstream_gene_variant ; 1278.0bp to feature; MODIFIER | N | Average:63.69; most accessible tissue: Minghui63 root, score: 88.106 | N | N | N | N |
| vg1223515373 | CCATAAGACAAAAAAAAAGTTGT -> C | LOC_Os12g38280.1 | downstream_gene_variant ; 4793.0bp to feature; MODIFIER | N | Average:63.69; most accessible tissue: Minghui63 root, score: 88.106 | N | N | N | N |
| vg1223515373 | CCATAAGACAAAAAAAAAGTTGT -> C | LOC_Os12g38290.1 | downstream_gene_variant ; 1897.0bp to feature; MODIFIER | N | Average:63.69; most accessible tissue: Minghui63 root, score: 88.106 | N | N | N | N |
| vg1223515373 | CCATAAGACAAAAAAAAAGTTGT -> C | LOC_Os12g38320.1 | downstream_gene_variant ; 4594.0bp to feature; MODIFIER | N | Average:63.69; most accessible tissue: Minghui63 root, score: 88.106 | N | N | N | N |
| vg1223515373 | CCATAAGACAAAAAAAAAGTTGT -> C | LOC_Os12g38300.1 | intron_variant ; MODIFIER | N | Average:63.69; most accessible tissue: Minghui63 root, score: 88.106 | N | N | N | N |