| Variant ID: vg0125055835 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 25055835 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CTTATAACCTGGAATGGAGGTAGTACAATTTTGATGAAGTTGCAAAATATTCGTTTTGCTATATTTTTAAAGTGTCGATTCAATCAAACCAAATATTTGA[C/A]
AATACCTTTTCTTTACAAACTAAATGGAGAATTAATTTATTGATATGGCTAAATTATTTTTTGGTGGCATGGTTGATTGGTATAAACCAAACATGCCATT
AATGGCATGTTTGGTTTATACCAATCAACCATGCCACCAAAAAATAATTTAGCCATATCAATAAATTAATTCTCCATTTAGTTTGTAAAGAAAAGGTATT[G/T]
TCAAATATTTGGTTTGATTGAATCGACACTTTAAAAATATAGCAAAACGAATATTTTGCAACTTCATCAAAATTGTACTACCTCCATTCCAGGTTATAAG
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 97.10% | 2.00% | 0.23% | 0.61% | NA |
| All Indica | 2759 | 99.80% | 0.10% | 0.00% | 0.04% | NA |
| All Japonica | 1512 | 94.90% | 2.60% | 0.66% | 1.85% | 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 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.70% | 0.10% | 0.00% | 0.13% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 85.50% | 7.10% | 1.79% | 5.56% | NA |
| Japonica Intermediate | 241 | 98.30% | 1.20% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 47.90% | 52.10% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 96.70% | 2.20% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0125055835 | C -> A | LOC_Os01g43720.1 | 3_prime_UTR_variant ; 713.0bp to feature; MODIFIER | silent_mutation | Average:63.314; most accessible tissue: Zhenshan97 root, score: 88.851 | N | N | N | N |
| vg0125055835 | C -> A | LOC_Os01g43740.1 | upstream_gene_variant ; 4929.0bp to feature; MODIFIER | silent_mutation | Average:63.314; most accessible tissue: Zhenshan97 root, score: 88.851 | N | N | N | N |
| vg0125055835 | C -> DEL | N | N | silent_mutation | Average:63.314; most accessible tissue: Zhenshan97 root, score: 88.851 | N | N | N | N |