| Variant ID: vg0100791466 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 791466 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TTCTTTTGCTGATGGTGGGCACAACAATCTATCTTTCACTAAAGACAAGATATAATGAAGAGATACATTTGAAGGTCGAAATGTTTCTCAAGACATATGG[C/A]
ACATCGAAACCCACAAGGTATAGTTTCTCTGAAGTTAAGAAGATTACAAGACGGTTCAGGGAAAAGATAGGCCACGGTGGGTATGGAAATGTATACAAGG
CCTTGTATACATTTCCATACCCACCGTGGCCTATCTTTTCCCTGAACCGTCTTGTAATCTTCTTAACTTCAGAGAAACTATACCTTGTGGGTTTCGATGT[G/T]
CCATATGTCTTGAGAAACATTTCGACCTTCAAATGTATCTCTTCATTATATCTTGTCTTTAGTGAAAGATAGATTGTTGTGCCCACCATCAGCAAAAGAA
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 56.30% | 1.20% | 2.16% | 40.31% | NA |
| All Indica | 2759 | 50.10% | 1.50% | 2.57% | 45.78% | NA |
| All Japonica | 1512 | 73.00% | 0.10% | 1.19% | 25.66% | NA |
| Aus | 269 | 36.80% | 5.20% | 1.86% | 56.13% | NA |
| Indica I | 595 | 69.10% | 0.70% | 0.84% | 29.41% | NA |
| Indica II | 465 | 75.90% | 0.00% | 1.08% | 23.01% | NA |
| Indica III | 913 | 18.60% | 3.40% | 2.74% | 75.25% | NA |
| Indica Intermediate | 786 | 57.10% | 0.90% | 4.58% | 37.40% | NA |
| Temperate Japonica | 767 | 70.10% | 0.30% | 1.56% | 28.03% | NA |
| Tropical Japonica | 504 | 83.10% | 0.00% | 0.40% | 16.47% | NA |
| Japonica Intermediate | 241 | 61.00% | 0.00% | 1.66% | 37.34% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0100791466 | C -> A | LOC_Os01g02440.1 | synonymous_variant ; p.Gly247Gly; LOW | synonymous_codon | Average:52.9; most accessible tissue: Zhenshan97 panicle, score: 67.02 | N | N | N | N |
| vg0100791466 | C -> DEL | LOC_Os01g02440.1 | N | frameshift_variant | Average:52.9; most accessible tissue: Zhenshan97 panicle, score: 67.02 | N | N | N | N |