| Variant ID: vg0512045460 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 12045460 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
GCGGCGGTGCTTCTCCCTTCAATGCGGCTAATTCCTTCTCCAAACGATCCACCTTGTCTTCTAGCTTGCAAATCTTACCACGATTCCGGTCTTCACGATC[T/C]
TGAGCGGCTAACACAGTCTCCGCACGACTTTCATCCATAGCCCACAACATCTCAACCAAATGCTTCGTGGTAGCATCATTCTCAATTCCTTCAGTCTCAA
TTGAGACTGAAGGAATTGAGAATGATGCTACCACGAAGCATTTGGTTGAGATGTTGTGGGCTATGGATGAAAGTCGTGCGGAGACTGTGTTAGCCGCTCA[A/G]
GATCGTGAAGACCGGAATCGTGGTAAGATTTGCAAGCTAGAAGACAAGGTGGATCGTTTGGAGAAGGAATTAGCCGCATTGAAGGGAGAAGCACCGCCGC
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 82.10% | 0.90% | 5.76% | 11.28% | NA |
| All Indica | 2759 | 85.90% | 1.50% | 7.83% | 4.82% | NA |
| All Japonica | 1512 | 84.90% | 0.10% | 3.11% | 11.97% | NA |
| Aus | 269 | 21.90% | 0.00% | 0.37% | 77.70% | NA |
| Indica I | 595 | 91.40% | 0.30% | 8.24% | 0.00% | NA |
| Indica II | 465 | 97.60% | 0.00% | 0.65% | 1.72% | NA |
| Indica III | 913 | 76.30% | 3.70% | 11.39% | 8.54% | NA |
| Indica Intermediate | 786 | 85.80% | 0.60% | 7.63% | 5.98% | NA |
| Temperate Japonica | 767 | 72.50% | 0.00% | 5.61% | 21.90% | NA |
| Tropical Japonica | 504 | 99.20% | 0.20% | 0.00% | 0.60% | 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% | 5.56% | 10.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0512045460 | T -> DEL | LOC_Os05g20520.1 | N | frameshift_variant | Average:12.233; most accessible tissue: Zhenshan97 flower, score: 24.143 | N | N | N | N |
| vg0512045460 | T -> C | LOC_Os05g20520.1 | synonymous_variant ; p.Gln174Gln; LOW | synonymous_codon | Average:12.233; most accessible tissue: Zhenshan97 flower, score: 24.143 | N | N | N | N |