| Variant ID: vg0131447880 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 31447880 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GCTTCCAGAAGTCGCGCCACCTCCTCGCGGATGAAGGCTTGACGTTCCGGGGCCTGCCGCCGCACTTTCTGCCGGACCGGCCTTGCGCCCGGCCGCACGG[C/T]
GAGACGGTGCTCAATCACCTCCCTGGGGACCCCGGGCATATCCGCCGGTCTCCATGCGAAGACGTCAGCGTTTGCCCGCAGGAAGGAGACGAGCGCGTGG
CCACGCGCTCGTCTCCTTCCTGCGGGCAAACGCTGACGTCTTCGCATGGAGACCGGCGGATATGCCCGGGGTCCCCAGGGAGGTGATTGAGCACCGTCTC[G/A]
CCGTGCGGCCGGGCGCAAGGCCGGTCCGGCAGAAAGTGCGGCGGCAGGCCCCGGAACGTCAAGCCTTCATCCGCGAGGAGGTGGCGCGACTTCTGGAAGC
| 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 | 47.90% | 0.20% | 7.36% | 44.54% | NA |
| All Indica | 2759 | 36.80% | 0.30% | 10.40% | 52.52% | NA |
| All Japonica | 1512 | 68.70% | 0.00% | 3.04% | 28.24% | NA |
| Aus | 269 | 23.00% | 0.00% | 2.97% | 73.98% | NA |
| Indica I | 595 | 23.00% | 0.70% | 9.92% | 66.39% | NA |
| Indica II | 465 | 24.50% | 0.20% | 8.82% | 66.45% | NA |
| Indica III | 913 | 54.80% | 0.00% | 9.31% | 35.93% | NA |
| Indica Intermediate | 786 | 33.60% | 0.40% | 12.98% | 53.05% | NA |
| Temperate Japonica | 767 | 60.60% | 0.00% | 3.52% | 35.85% | NA |
| Tropical Japonica | 504 | 90.70% | 0.00% | 1.19% | 8.13% | NA |
| Japonica Intermediate | 241 | 48.50% | 0.00% | 5.39% | 46.06% | NA |
| VI/Aromatic | 96 | 94.80% | 0.00% | 3.12% | 2.08% | NA |
| Intermediate | 90 | 64.40% | 0.00% | 4.44% | 31.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0131447880 | C -> T | LOC_Os01g54650.1 | downstream_gene_variant ; 4253.0bp to feature; MODIFIER | silent_mutation | Average:27.392; most accessible tissue: Zhenshan97 panicle, score: 61.671 | N | N | N | N |
| vg0131447880 | C -> T | LOC_Os01g54660.1 | intron_variant ; MODIFIER | silent_mutation | Average:27.392; most accessible tissue: Zhenshan97 panicle, score: 61.671 | N | N | N | N |
| vg0131447880 | C -> DEL | N | N | silent_mutation | Average:27.392; most accessible tissue: Zhenshan97 panicle, score: 61.671 | N | N | N | N |