| Variant ID: vg0139512288 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 39512288 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CGAAACATAAACACATCGATAAGTTCGAAACGAATTACAAGCAAATCCACATGCCGACATAGAACATAAGAACTACACCACGTAGCCAGACGTGGCACGA[C/T]
GACGCCTAGGACGTGGTCGAGTGGAGGTAGTGCCTTCACCCGTAGGGCGAGCTCCATCTGCTGCTGATCCTGATAGTCCTGCCTCCGCCGCACTTGGTTT
AAACCAAGTGCGGCGGAGGCAGGACTATCAGGATCAGCAGCAGATGGAGCTCGCCCTACGGGTGAAGGCACTACCTCCACTCGACCACGTCCTAGGCGTC[G/A]
TCGTGCCACGTCTGGCTACGTGGTGTAGTTCTTATGTTCTATGTCGGCATGTGGATTTGCTTGTAATTCGTTTCGAACTTATCGATGTGTTTATGTTTCG
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 26.70% | 0.50% | 0.44% | 72.32% | NA |
| All Indica | 2759 | 2.20% | 0.80% | 0.69% | 96.30% | NA |
| All Japonica | 1512 | 74.80% | 0.00% | 0.07% | 25.13% | NA |
| Aus | 269 | 2.20% | 0.00% | 0.00% | 97.77% | NA |
| Indica I | 595 | 2.90% | 0.20% | 1.01% | 95.97% | NA |
| Indica II | 465 | 1.50% | 0.00% | 0.86% | 97.63% | NA |
| Indica III | 913 | 1.40% | 0.20% | 0.00% | 98.36% | NA |
| Indica Intermediate | 786 | 2.90% | 2.50% | 1.15% | 93.38% | NA |
| Temperate Japonica | 767 | 97.30% | 0.00% | 0.00% | 2.74% | NA |
| Tropical Japonica | 504 | 52.60% | 0.00% | 0.20% | 47.22% | NA |
| Japonica Intermediate | 241 | 49.80% | 0.00% | 0.00% | 50.21% | NA |
| VI/Aromatic | 96 | 25.00% | 0.00% | 1.04% | 73.96% | NA |
| Intermediate | 90 | 47.80% | 0.00% | 0.00% | 52.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0139512288 | C -> T | LOC_Os01g67990.1 | missense_variant ; p.Arg869His; MODERATE | nonsynonymous_codon ; R869H | Average:7.548; most accessible tissue: Callus, score: 21.029 | unknown | unknown | DELETERIOUS | 0.01 |
| vg0139512288 | C -> DEL | LOC_Os01g67990.1 | N | frameshift_variant | Average:7.548; most accessible tissue: Callus, score: 21.029 | N | N | N | N |