| Variant ID: vg0136517574 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 36517574 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
TCTTTATAGCTTTATGAGGACATATTTATGGTGGAGTGCGGTGTGTGCGGATATGAAAGCATTATGTACCTCTGTAATAGGGTTCAGAAGACGACGACCA[T/C]
CGTAGTTCACCATATAGTTGAATACGTAAAAGCCACAGTCATCCCTGTATGTTTTTGAGAAAGTAGTGTCAGTACAAGCTTTGGGTTGGTTGTATTTCGT
ACGAAATACAACCAACCCAAAGCTTGTACTGACACTACTTTCTCAAAAACATACAGGGATGACTGTGGCTTTTACGTATTCAACTATATGGTGAACTACG[A/G]
TGGTCGTCGTCTTCTGAACCCTATTACAGAGGTACATAATGCTTTCATATCCGCACACACCGCACTCCACCATAAATATGTCCTCATAAAGCTATAAAGA
| 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 | 36.90% | 0.10% | 7.49% | 55.50% | NA |
| All Indica | 2759 | 4.20% | 0.00% | 7.97% | 87.82% | NA |
| All Japonica | 1512 | 97.00% | 0.40% | 1.19% | 1.46% | NA |
| Aus | 269 | 3.30% | 0.00% | 40.89% | 55.76% | NA |
| Indica I | 595 | 2.50% | 0.00% | 5.71% | 91.76% | NA |
| Indica II | 465 | 3.70% | 0.00% | 4.73% | 91.61% | NA |
| Indica III | 913 | 2.60% | 0.00% | 10.30% | 87.08% | NA |
| Indica Intermediate | 786 | 7.60% | 0.00% | 8.91% | 83.46% | NA |
| Temperate Japonica | 767 | 96.90% | 0.80% | 1.43% | 0.91% | NA |
| Tropical Japonica | 504 | 97.00% | 0.00% | 0.99% | 1.98% | NA |
| Japonica Intermediate | 241 | 97.10% | 0.00% | 0.83% | 2.07% | NA |
| VI/Aromatic | 96 | 92.70% | 0.00% | 1.04% | 6.25% | NA |
| Intermediate | 90 | 70.00% | 0.00% | 5.56% | 24.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0136517574 | T -> DEL | LOC_Os01g63040.1 | N | frameshift_variant | Average:4.359; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0136517574 | T -> C | LOC_Os01g63040.1 | missense_variant ; p.Asp827Gly; MODERATE | nonsynonymous_codon ; D827G | Average:4.359; most accessible tissue: Minghui63 panicle, score: 7.125 | unknown | unknown | DELETERIOUS | 0.02 |