| Variant ID: vg0123776551 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 23776551 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
CTCAACGAGGGTTGCATTGCATTGCGTAGCGTGGACTATCACTAACACACAATGGCTAGAATGGCTAGAACTCCAGTTCATCCACGATCGTCCTCGATTG[T/C]
AGCTGCATTCACTTACCTTTTGCTAGTCCTCTTCCGAGACGCCATCACCACCGCAGCTGCATCTCCCAAAGCTCCGGCATCCACCAATGGCTGCATTGCA
TGCAATGCAGCCATTGGTGGATGCCGGAGCTTTGGGAGATGCAGCTGCGGTGGTGATGGCGTCTCGGAAGAGGACTAGCAAAAGGTAAGTGAATGCAGCT[A/G]
CAATCGAGGACGATCGTGGATGAACTGGAGTTCTAGCCATTCTAGCCATTGTGTGTTAGTGATAGTCCACGCTACGCAATGCAATGCAACCCTCGTTGAG
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 43.50% | 0.10% | 0.15% | 56.26% | NA |
| All Indica | 2759 | 9.80% | 0.00% | 0.18% | 89.96% | NA |
| All Japonica | 1512 | 92.10% | 0.00% | 0.00% | 7.94% | NA |
| Aus | 269 | 92.20% | 0.00% | 0.00% | 7.81% | NA |
| Indica I | 595 | 2.50% | 0.00% | 0.34% | 97.14% | NA |
| Indica II | 465 | 6.00% | 0.00% | 0.00% | 93.98% | NA |
| Indica III | 913 | 11.20% | 0.00% | 0.11% | 88.72% | NA |
| Indica Intermediate | 786 | 16.00% | 0.10% | 0.25% | 83.59% | NA |
| Temperate Japonica | 767 | 99.50% | 0.00% | 0.00% | 0.52% | NA |
| Tropical Japonica | 504 | 79.00% | 0.00% | 0.00% | 21.03% | NA |
| Japonica Intermediate | 241 | 95.90% | 0.00% | 0.00% | 4.15% | NA |
| VI/Aromatic | 96 | 99.00% | 0.00% | 0.00% | 1.04% | NA |
| Intermediate | 90 | 56.70% | 2.20% | 2.22% | 38.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0123776551 | T -> DEL | LOC_Os01g41930.1 | N | frameshift_variant | Average:69.708; most accessible tissue: Minghui63 root, score: 86.159 | N | N | N | N |
| vg0123776551 | T -> C | LOC_Os01g41930.1 | missense_variant ; p.Val17Ala; MODERATE | nonsynonymous_codon ; V17A | Average:69.708; most accessible tissue: Minghui63 root, score: 86.159 | unknown | unknown | TOLERATED | 0.28 |