| Variant ID: vg0131447860 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 31447860 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TGACCTCACGGATGAATCCGGCTTCCAGAAGTCGCGCCACCTCCTCGCGGATGAAGGCTTGACGTTCCGGGGCCTGCCGCCGCACTTTCTGCCGGACCGG[C/T]
CTTGCGCCCGGCCGCACGGCGAGACGGTGCTCAATCACCTCCCTGGGGACCCCGGGCATATCCGCCGGTCTCCATGCGAAGACGTCAGCGTTTGCCCGCA
TGCGGGCAAACGCTGACGTCTTCGCATGGAGACCGGCGGATATGCCCGGGGTCCCCAGGGAGGTGATTGAGCACCGTCTCGCCGTGCGGCCGGGCGCAAG[G/A]
CCGGTCCGGCAGAAAGTGCGGCGGCAGGCCCCGGAACGTCAAGCCTTCATCCGCGAGGAGGTGGCGCGACTTCTGGAAGCCGGATTCATCCGTGAGGTCA
| 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 | 51.20% | 0.40% | 4.00% | 44.37% | NA |
| All Indica | 2759 | 42.90% | 0.70% | 5.73% | 50.71% | NA |
| All Japonica | 1512 | 68.90% | 0.00% | 0.53% | 30.56% | NA |
| Aus | 269 | 17.50% | 0.70% | 6.69% | 75.09% | NA |
| Indica I | 595 | 30.10% | 0.70% | 5.55% | 63.70% | NA |
| Indica II | 465 | 30.30% | 0.20% | 4.09% | 65.38% | NA |
| Indica III | 913 | 59.10% | 1.20% | 5.37% | 34.28% | NA |
| Indica Intermediate | 786 | 41.10% | 0.40% | 7.25% | 51.27% | NA |
| Temperate Japonica | 767 | 59.70% | 0.00% | 0.52% | 39.77% | NA |
| Tropical Japonica | 504 | 91.10% | 0.00% | 0.20% | 8.73% | NA |
| Japonica Intermediate | 241 | 51.90% | 0.00% | 1.24% | 46.89% | NA |
| VI/Aromatic | 96 | 92.70% | 0.00% | 2.08% | 5.21% | NA |
| Intermediate | 90 | 64.40% | 0.00% | 3.33% | 32.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0131447860 | C -> T | LOC_Os01g54660.1 | splice_region_variant&synonymous_variant ; p.Arg825Arg; LOW | synonymous_codon | Average:25.886; most accessible tissue: Zhenshan97 panicle, score: 59.59 | N | N | N | N |
| vg0131447860 | C -> DEL | LOC_Os01g54660.1 | N | frameshift_variant | Average:25.886; most accessible tissue: Zhenshan97 panicle, score: 59.59 | N | N | N | N |