| Variant ID: vg0512023277 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 12023277 |
| Reference Allele: A | Alternative Allele: C |
| Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
GACACTTGTCAGCATAATGTCCTGGATCTCCACAGTTGAAACACACCACGGGCTTGTTGCCTTGCTCCCTCTTGGCAGGTTGTTGCTGTGCTGGAGCTGC[A/C]
ACAGGACGTGGAGCTTGATTACGGATGTTGTTGCCAGCATTGTTGTTGAAGAACTGACGCTGCGGACGAACAACAGACGAAGAACCTCCCTGTGGCATGG
CCATGCCACAGGGAGGTTCTTCGTCTGTTGTTCGTCCGCAGCGTCAGTTCTTCAACAACAATGCTGGCAACAACATCCGTAATCAAGCTCCACGTCCTGT[T/G]
GCAGCTCCAGCACAGCAACAACCTGCCAAGAGGGAGCAAGGCAACAAGCCCGTGGTGTGTTTCAACTGTGGAGATCCAGGACATTATGCTGACAAGTGTC
| Populations | Population Size | Frequency of A(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 93.70% | 0.30% | 2.77% | 3.26% | NA |
| All Indica | 2759 | 93.40% | 0.50% | 3.41% | 2.68% | NA |
| All Japonica | 1512 | 99.80% | 0.00% | 0.07% | 0.13% | NA |
| Aus | 269 | 59.50% | 0.00% | 12.27% | 28.25% | NA |
| Indica I | 595 | 95.00% | 0.00% | 4.54% | 0.50% | NA |
| Indica II | 465 | 98.90% | 0.00% | 0.86% | 0.22% | NA |
| Indica III | 913 | 91.70% | 1.20% | 3.18% | 3.94% | NA |
| Indica Intermediate | 786 | 91.00% | 0.40% | 4.33% | 4.33% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.40% | 0.00% | 0.20% | 0.40% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 0.00% | 0.00% | 1.04% | NA |
| Intermediate | 90 | 95.60% | 0.00% | 3.33% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0512023277 | A -> DEL | LOC_Os05g20480.1 | N | frameshift_variant | Average:28.005; most accessible tissue: Zhenshan97 flag leaf, score: 43.728 | N | N | N | N |
| vg0512023277 | A -> C | LOC_Os05g20480.1 | synonymous_variant ; p.Val62Val; LOW | synonymous_codon | Average:28.005; most accessible tissue: Zhenshan97 flag leaf, score: 43.728 | N | N | N | N |