| Variant ID: vg0100791442 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 791442 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CATCCTCAGCAGCCACACTAGTTGTTCTTTTGCTGATGGTGGGCACAACAATCTATCTTTCACTAAAGACAAGATATAATGAAGAGATACATTTGAAGGT[C/T]
GAAATGTTTCTCAAGACATATGGCACATCGAAACCCACAAGGTATAGTTTCTCTGAAGTTAAGAAGATTACAAGACGGTTCAGGGAAAAGATAGGCCACG
CGTGGCCTATCTTTTCCCTGAACCGTCTTGTAATCTTCTTAACTTCAGAGAAACTATACCTTGTGGGTTTCGATGTGCCATATGTCTTGAGAAACATTTC[G/A]
ACCTTCAAATGTATCTCTTCATTATATCTTGTCTTTAGTGAAAGATAGATTGTTGTGCCCACCATCAGCAAAAGAACAACTAGTGTGGCTGCTGAGGATG
| 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 | 56.70% | 1.20% | 1.95% | 40.20% | NA |
| All Indica | 2759 | 50.50% | 1.40% | 2.32% | 45.74% | NA |
| All Japonica | 1512 | 73.30% | 0.10% | 1.12% | 25.46% | NA |
| Aus | 269 | 37.20% | 5.20% | 1.86% | 55.76% | NA |
| Indica I | 595 | 69.40% | 0.70% | 0.84% | 29.08% | NA |
| Indica II | 465 | 76.10% | 0.00% | 0.86% | 23.01% | NA |
| Indica III | 913 | 19.20% | 3.20% | 2.52% | 75.14% | NA |
| Indica Intermediate | 786 | 57.40% | 0.90% | 4.07% | 37.66% | NA |
| Temperate Japonica | 767 | 70.70% | 0.10% | 1.43% | 27.77% | NA |
| Tropical Japonica | 504 | 83.30% | 0.00% | 0.40% | 16.27% | NA |
| Japonica Intermediate | 241 | 61.00% | 0.00% | 1.66% | 37.34% | NA |
| VI/Aromatic | 96 | 13.50% | 0.00% | 3.12% | 83.33% | NA |
| Intermediate | 90 | 71.10% | 0.00% | 3.33% | 25.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0100791442 | C -> T | LOC_Os01g02440.1 | synonymous_variant ; p.Val239Val; LOW | synonymous_codon | Average:51.277; most accessible tissue: Zhenshan97 panicle, score: 65.386 | N | N | N | N |
| vg0100791442 | C -> DEL | LOC_Os01g02440.1 | N | frameshift_variant | Average:51.277; most accessible tissue: Zhenshan97 panicle, score: 65.386 | N | N | N | N |