| Variant ID: vg0135290677 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 35290677 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 236. )
ATCAAGATCAGCTTCGTAGAGATGACCTCGACTACTTGGAAGAGCGAAGGCGGCGCGCGGCCCTCCGAGCTGCGCGCTACCAGCAGAGCCTGCGGCGCTA[C/T]
CATCAGCGCCACGTCCGGGCCCGATCACTCTGCGTCGACGACCTCGTCCTACGCCGCGTCCAAACGCGTGCTGGATTGAGCAAACTCTCACCGATGTGGG
CCCACATCGGTGAGAGTTTGCTCAATCCAGCACGCGTTTGGACGCGGCGTAGGACGAGGTCGTCGACGCAGAGTGATCGGGCCCGGACGTGGCGCTGATG[G/A]
TAGCGCCGCAGGCTCTGCTGGTAGCGCGCAGCTCGGAGGGCCGCGCGCCGCCTTCGCTCTTCCAAGTAGTCGAGGTCATCTCTACGAAGCTGATCTTGAT
| 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 | 19.00% | 0.20% | 8.89% | 71.88% | NA |
| All Indica | 2759 | 1.40% | 0.10% | 4.10% | 94.31% | NA |
| All Japonica | 1512 | 50.40% | 0.00% | 16.27% | 33.33% | NA |
| Aus | 269 | 0.00% | 2.60% | 11.90% | 85.50% | NA |
| Indica I | 595 | 1.00% | 0.00% | 4.20% | 94.79% | NA |
| Indica II | 465 | 0.00% | 0.00% | 0.43% | 99.57% | NA |
| Indica III | 913 | 1.90% | 0.00% | 5.48% | 92.66% | NA |
| Indica Intermediate | 786 | 2.20% | 0.50% | 4.58% | 92.75% | NA |
| Temperate Japonica | 767 | 43.90% | 0.00% | 17.73% | 38.33% | NA |
| Tropical Japonica | 504 | 48.40% | 0.00% | 18.45% | 33.13% | NA |
| Japonica Intermediate | 241 | 75.10% | 0.00% | 7.05% | 17.84% | NA |
| VI/Aromatic | 96 | 77.10% | 0.00% | 10.42% | 12.50% | NA |
| Intermediate | 90 | 24.40% | 0.00% | 21.11% | 54.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0135290677 | C -> T | LOC_Os01g60990.1 | synonymous_variant ; p.Tyr356Tyr; LOW | synonymous_codon | Average:37.806; most accessible tissue: Zhenshan97 panicle, score: 57.341 | N | N | N | N |
| vg0135290677 | C -> DEL | LOC_Os01g60990.1 | N | frameshift_variant | Average:37.806; most accessible tissue: Zhenshan97 panicle, score: 57.341 | N | N | N | N |