| Variant ID: vg0108457584 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 8457584 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: Unkown |
Inferred Ancestral Allele: Not determined.
AAGCCTACATACGCCAAGACACGCCGCCGGATATCGACTTGAAGGATAGGCATGGCTATTCCCCTACGGTGTCTCCGGATACCGTCAGGAGATACGAAAG[C/T]
GCTATCTCTGATCTCGCCGGGCACAGATTCGAGGAGGAAGACTACCCTGTTGTCGACTACGAGTCAGACCTTCAGACCGACATGTCCACAACAGTTAGAT
ATCTAACTGTTGTGGACATGTCGGTCTGAAGGTCTGACTCGTAGTCGACAACAGGGTAGTCTTCCTCCTCGAATCTGTGCCCGGCGAGATCAGAGATAGC[G/A]
CTTTCGTATCTCCTGACGGTATCCGGAGACACCGTAGGGGAATAGCCATGCCTATCCTTCAAGTCGATATCCGGCGGCGTGTCTTGGCGTATGTAGGCTT
| Populations | Population Size | Frequency of C(primary allele) | Frequency of Unkown(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 98.90% | 0.00% | 0.57% | 0.51% | NA |
| All Indica | 2759 | 98.20% | 0.00% | 0.98% | 0.80% | NA |
| All Japonica | 1512 | 99.90% | 0.00% | 0.00% | 0.07% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.00% | 0.00% | 0.67% | 0.34% | NA |
| Indica II | 465 | 93.30% | 0.00% | 3.23% | 3.44% | NA |
| Indica III | 913 | 99.80% | 0.00% | 0.11% | 0.11% | NA |
| Indica Intermediate | 786 | 98.70% | 0.00% | 0.89% | 0.38% | NA |
| Temperate Japonica | 767 | 99.90% | 0.00% | 0.00% | 0.13% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 98.90% | 0.00% | 0.00% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0108457584 | C -> T | LOC_Os01g15070.1 | synonymous_variant ; p.Ser53Ser; LOW | N | Average:55.664; most accessible tissue: Zhenshan97 root, score: 68.908 | N | N | N | N |
| vg0108457584 | C -> T | LOC_Os01g15080.1 | upstream_gene_variant ; 375.0bp to feature; MODIFIER | N | Average:55.664; most accessible tissue: Zhenshan97 root, score: 68.908 | N | N | N | N |
| vg0108457584 | C -> T | LOC_Os01g15090.1 | upstream_gene_variant ; 3488.0bp to feature; MODIFIER | N | Average:55.664; most accessible tissue: Zhenshan97 root, score: 68.908 | N | N | N | N |
| vg0108457584 | C -> T | LOC_Os01g15060.1 | downstream_gene_variant ; 1562.0bp to feature; MODIFIER | N | Average:55.664; most accessible tissue: Zhenshan97 root, score: 68.908 | N | N | N | N |