| Variant ID: vg0100791451 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 791451 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
CAGCCACACTAGTTGTTCTTTTGCTGATGGTGGGCACAACAATCTATCTTTCACTAAAGACAAGATATAATGAAGAGATACATTTGAAGGTCGAAATGTT[T/C]
CTCAAGACATATGGCACATCGAAACCCACAAGGTATAGTTTCTCTGAAGTTAAGAAGATTACAAGACGGTTCAGGGAAAAGATAGGCCACGGTGGGTATG
CATACCCACCGTGGCCTATCTTTTCCCTGAACCGTCTTGTAATCTTCTTAACTTCAGAGAAACTATACCTTGTGGGTTTCGATGTGCCATATGTCTTGAG[A/G]
AACATTTCGACCTTCAAATGTATCTCTTCATTATATCTTGTCTTTAGTGAAAGATAGATTGTTGTGCCCACCATCAGCAAAAGAACAACTAGTGTGGCTG
| 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 | 56.60% | 1.20% | 1.99% | 40.27% | NA |
| All Indica | 2759 | 50.40% | 1.40% | 2.39% | 45.78% | NA |
| All Japonica | 1512 | 73.30% | 0.10% | 0.99% | 25.60% | NA |
| Aus | 269 | 37.20% | 5.20% | 1.86% | 55.76% | NA |
| Indica I | 595 | 69.40% | 0.70% | 0.67% | 29.24% | NA |
| Indica II | 465 | 76.10% | 0.00% | 0.86% | 23.01% | NA |
| Indica III | 913 | 19.10% | 3.20% | 2.52% | 75.25% | NA |
| Indica Intermediate | 786 | 57.10% | 0.90% | 4.45% | 37.53% | NA |
| Temperate Japonica | 767 | 70.70% | 0.10% | 1.30% | 27.90% | NA |
| Tropical Japonica | 504 | 83.30% | 0.00% | 0.40% | 16.27% | NA |
| Japonica Intermediate | 241 | 61.00% | 0.00% | 1.24% | 37.76% | NA |
| VI/Aromatic | 96 | 11.50% | 0.00% | 5.21% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0100791451 | T -> DEL | LOC_Os01g02440.1 | N | frameshift_variant | Average:51.47; most accessible tissue: Zhenshan97 panicle, score: 67.02 | N | N | N | N |
| vg0100791451 | T -> C | LOC_Os01g02440.1 | synonymous_variant ; p.Phe242Phe; LOW | synonymous_codon | Average:51.47; most accessible tissue: Zhenshan97 panicle, score: 67.02 | N | N | N | N |