| Variant ID: vg0125055841 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr01 | Position: 25055841 |
| Reference Allele: CT | Alternative Allele: C |
| Primary Allele: CT | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
ACCTGGAATGGAGGTAGTACAATTTTGATGAAGTTGCAAAATATTCGTTTTGCTATATTTTTAAAGTGTCGATTCAATCAAACCAAATATTTGACAATAC[CT/C]
TTTCTTTACAAACTAAATGGAGAATTAATTTATTGATATGGCTAAATTATTTTTTGGTGGCATGGTTGATTGGTATAAACCAAACATGCCATTTTTTTTA
TAAAAAAAATGGCATGTTTGGTTTATACCAATCAACCATGCCACCAAAAAATAATTTAGCCATATCAATAAATTAATTCTCCATTTAGTTTGTAAAGAAA[AG/G]
GTATTGTCAAATATTTGGTTTGATTGAATCGACACTTTAAAAATATAGCAAAACGAATATTTTGCAACTTCATCAAAATTGTACTACCTCCATTCCAGGT
| Populations | Population Size | Frequency of CT(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 97.10% | 2.90% | 0.00% | 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 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 91.50% | 8.50% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 97.80% | 2.20% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0125055841 | CT -> C | LOC_Os01g43720.1 | 3_prime_UTR_variant ; 706.0bp to feature; MODIFIER | silent_mutation | Average:63.473; most accessible tissue: Zhenshan97 root, score: 88.924 | N | N | N | N |
| vg0125055841 | CT -> C | LOC_Os01g43740.1 | upstream_gene_variant ; 4922.0bp to feature; MODIFIER | silent_mutation | Average:63.473; most accessible tissue: Zhenshan97 root, score: 88.924 | N | N | N | N |