| Variant ID: vg0131447836 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 31447836 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GGTTCGCCAGCCACTCCGGATGGATGACCTCACGGATGAATCCGGCTTCCAGAAGTCGCGCCACCTCCTCGCGGATGAAGGCTTGACGTTCCGGGGCCTG[C/T]
CGCCGCACTTTCTGCCGGACCGGCCTTGCGCCCGGCCGCACGGCGAGACGGTGCTCAATCACCTCCCTGGGGACCCCGGGCATATCCGCCGGTCTCCATG
CATGGAGACCGGCGGATATGCCCGGGGTCCCCAGGGAGGTGATTGAGCACCGTCTCGCCGTGCGGCCGGGCGCAAGGCCGGTCCGGCAGAAAGTGCGGCG[G/A]
CAGGCCCCGGAACGTCAAGCCTTCATCCGCGAGGAGGTGGCGCGACTTCTGGAAGCCGGATTCATCCGTGAGGTCATCCATCCGGAGTGGCTGGCGAACC
| 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 | 52.30% | 0.90% | 4.97% | 41.85% | NA |
| All Indica | 2759 | 42.90% | 1.50% | 5.40% | 50.20% | NA |
| All Japonica | 1512 | 70.60% | 0.00% | 5.09% | 24.27% | NA |
| Aus | 269 | 25.70% | 0.00% | 1.12% | 73.23% | NA |
| Indica I | 595 | 28.10% | 2.70% | 5.71% | 63.53% | NA |
| Indica II | 465 | 28.20% | 1.50% | 5.16% | 65.16% | NA |
| Indica III | 913 | 62.20% | 0.10% | 4.49% | 33.19% | NA |
| Indica Intermediate | 786 | 40.30% | 2.30% | 6.36% | 51.02% | NA |
| Temperate Japonica | 767 | 62.50% | 0.00% | 8.87% | 28.68% | NA |
| Tropical Japonica | 504 | 91.10% | 0.00% | 0.40% | 8.53% | NA |
| Japonica Intermediate | 241 | 53.90% | 0.00% | 2.90% | 43.15% | NA |
| VI/Aromatic | 96 | 94.80% | 0.00% | 2.08% | 3.12% | NA |
| Intermediate | 90 | 66.70% | 0.00% | 4.44% | 28.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0131447836 | C -> T | LOC_Os01g54660.1 | synonymous_variant ; p.Arg833Arg; LOW | synonymous_codon | Average:23.721; most accessible tissue: Zhenshan97 panicle, score: 52.263 | N | N | N | N |
| vg0131447836 | C -> DEL | LOC_Os01g54660.1 | N | frameshift_variant | Average:23.721; most accessible tissue: Zhenshan97 panicle, score: 52.263 | N | N | N | N |