| Variant ID: vg0128509434 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 28509434 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CAGGTGCCGTTGTACGGCGGTGCCAGATTGGGGTGTGACATATATGAACGATGGGAGGCGCGTGATGGTGGCGGTGTCTAGGCCGAACCTGGGCAGCGTC[G/A]
GCTGCTGCTGCTCCTGCTCCATGACCAGTGGACGATCACGCCGGCGACAGGCAATGCGGAGGGCTCGAGGGCAGATGAAGATGGTGATGAGGAAGAAGCT
AGCTTCTTCCTCATCACCATCTTCATCTGCCCTCGAGCCCTCCGCATTGCCTGTCGCCGGCGTGATCGTCCACTGGTCATGGAGCAGGAGCAGCAGCAGC[C/T]
GACGCTGCCCAGGTTCGGCCTAGACACCGCCACCATCACGCGCCTCCCATCGTTCATATATGTCACACCCCAATCTGGCACCGCCGTACAACGGCACCTG
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 57.90% | 0.10% | 11.85% | 30.11% | NA |
| All Indica | 2759 | 46.90% | 0.20% | 19.50% | 33.38% | NA |
| All Japonica | 1512 | 90.10% | 0.00% | 0.53% | 9.39% | NA |
| Aus | 269 | 2.60% | 0.00% | 2.23% | 95.17% | NA |
| Indica I | 595 | 24.70% | 0.00% | 22.35% | 52.94% | NA |
| Indica II | 465 | 47.30% | 0.00% | 32.04% | 20.65% | NA |
| Indica III | 913 | 65.80% | 0.50% | 9.31% | 24.32% | NA |
| Indica Intermediate | 786 | 41.60% | 0.00% | 21.76% | 36.64% | NA |
| Temperate Japonica | 767 | 93.10% | 0.00% | 0.26% | 6.65% | NA |
| Tropical Japonica | 504 | 82.30% | 0.00% | 0.99% | 16.67% | NA |
| Japonica Intermediate | 241 | 96.70% | 0.00% | 0.41% | 2.90% | NA |
| VI/Aromatic | 96 | 18.80% | 0.00% | 2.08% | 79.17% | NA |
| Intermediate | 90 | 62.20% | 0.00% | 6.67% | 31.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0128509434 | G -> A | LOC_Os01g49570.1 | missense_variant ; p.Pro47Leu; MODERATE | nonsynonymous_codon ; P47L | Average:24.383; most accessible tissue: Callus, score: 48.491 | unknown | unknown | DELETERIOUS | 0.04 |
| vg0128509434 | G -> DEL | LOC_Os01g49570.1 | N | frameshift_variant | Average:24.383; most accessible tissue: Callus, score: 48.491 | N | N | N | N |