| Variant ID: vg0131447818 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 31447818 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
CCTTGGGAACGACCACCGGGTTCGCCAGCCACTCCGGATGGATGACCTCACGGATGAATCCGGCTTCCAGAAGTCGCGCCACCTCCTCGCGGATGAAGGC[T/C]
TGACGTTCCGGGGCCTGCCGCCGCACTTTCTGCCGGACCGGCCTTGCGCCCGGCCGCACGGCGAGACGGTGCTCAATCACCTCCCTGGGGACCCCGGGCA
TGCCCGGGGTCCCCAGGGAGGTGATTGAGCACCGTCTCGCCGTGCGGCCGGGCGCAAGGCCGGTCCGGCAGAAAGTGCGGCGGCAGGCCCCGGAACGTCA[A/G]
GCCTTCATCCGCGAGGAGGTGGCGCGACTTCTGGAAGCCGGATTCATCCGTGAGGTCATCCATCCGGAGTGGCTGGCGAACCCGGTGGTCGTTCCCAAGG
| 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 | 54.50% | 0.20% | 5.12% | 40.16% | NA |
| All Indica | 2759 | 45.70% | 0.10% | 5.69% | 48.50% | NA |
| All Japonica | 1512 | 73.50% | 0.00% | 4.30% | 22.22% | NA |
| Aus | 269 | 18.60% | 3.00% | 5.20% | 73.23% | NA |
| Indica I | 595 | 33.60% | 0.00% | 5.04% | 61.34% | NA |
| Indica II | 465 | 31.60% | 0.00% | 7.74% | 60.65% | NA |
| Indica III | 913 | 62.40% | 0.00% | 4.49% | 33.08% | NA |
| Indica Intermediate | 786 | 43.90% | 0.30% | 6.36% | 49.49% | NA |
| Temperate Japonica | 767 | 67.80% | 0.00% | 6.91% | 25.29% | NA |
| Tropical Japonica | 504 | 91.10% | 0.00% | 0.40% | 8.53% | NA |
| Japonica Intermediate | 241 | 54.80% | 0.00% | 4.15% | 41.08% | NA |
| VI/Aromatic | 96 | 94.80% | 1.00% | 2.08% | 2.08% | NA |
| Intermediate | 90 | 67.80% | 0.00% | 4.44% | 27.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0131447818 | T -> DEL | LOC_Os01g54660.1 | N | frameshift_variant | Average:23.371; most accessible tissue: Zhenshan97 panicle, score: 52.263 | N | N | N | N |
| vg0131447818 | T -> C | LOC_Os01g54660.1 | synonymous_variant ; p.Gln839Gln; LOW | synonymous_codon | Average:23.371; most accessible tissue: Zhenshan97 panicle, score: 52.263 | N | N | N | N |