| Variant ID: vg0512045481 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 12045481 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
ATGCGGCTAATTCCTTCTCCAAACGATCCACCTTGTCTTCTAGCTTGCAAATCTTACCACGATTCCGGTCTTCACGATCTTGAGCGGCTAACACAGTCTC[C/T]
GCACGACTTTCATCCATAGCCCACAACATCTCAACCAAATGCTTCGTGGTAGCATCATTCTCAATTCCTTCAGTCTCAAGGTAACTGCCACGGTCACTTC
GAAGTGACCGTGGCAGTTACCTTGAGACTGAAGGAATTGAGAATGATGCTACCACGAAGCATTTGGTTGAGATGTTGTGGGCTATGGATGAAAGTCGTGC[G/A]
GAGACTGTGTTAGCCGCTCAAGATCGTGAAGACCGGAATCGTGGTAAGATTTGCAAGCTAGAAGACAAGGTGGATCGTTTGGAGAAGGAATTAGCCGCAT
| 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 | 82.10% | 0.30% | 5.01% | 12.61% | NA |
| All Indica | 2759 | 86.00% | 0.40% | 6.67% | 6.92% | NA |
| All Japonica | 1512 | 84.90% | 0.00% | 3.11% | 12.04% | NA |
| Aus | 269 | 21.60% | 0.00% | 0.37% | 78.07% | NA |
| Indica I | 595 | 91.60% | 0.00% | 8.24% | 0.17% | NA |
| Indica II | 465 | 97.60% | 0.00% | 0.65% | 1.72% | NA |
| Indica III | 913 | 76.50% | 1.10% | 9.75% | 12.71% | NA |
| Indica Intermediate | 786 | 85.90% | 0.30% | 5.47% | 8.40% | NA |
| Temperate Japonica | 767 | 72.50% | 0.00% | 5.61% | 21.90% | NA |
| Tropical Japonica | 504 | 99.20% | 0.00% | 0.00% | 0.79% | NA |
| Japonica Intermediate | 241 | 94.20% | 0.00% | 1.66% | 4.15% | NA |
| VI/Aromatic | 96 | 95.80% | 0.00% | 3.12% | 1.04% | NA |
| Intermediate | 90 | 84.40% | 0.00% | 2.22% | 13.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0512045481 | C -> T | LOC_Os05g20520.1 | synonymous_variant ; p.Ala167Ala; LOW | synonymous_codon | Average:11.469; most accessible tissue: Zhenshan97 flower, score: 24.143 | N | N | N | N |
| vg0512045481 | C -> DEL | LOC_Os05g20520.1 | N | frameshift_variant | Average:11.469; most accessible tissue: Zhenshan97 flower, score: 24.143 | N | N | N | N |