| Variant ID: vg0128509381 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 28509381 |
| Reference Allele: A | Alternative Allele: G,T |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
TCACGGTTTCGTAGGAAGCGGTTCGCGCCGTTTTTCCCACGACACGCTCCTGTCAGGTGCCGTTGTACGGCGGTGCCAGATTGGGGTGTGACATATATGA[A/G,T]
CGATGGGAGGCGCGTGATGGTGGCGGTGTCTAGGCCGAACCTGGGCAGCGTCGGCTGCTGCTGCTCCTGCTCCATGACCAGTGGACGATCACGCCGGCGA
TCGCCGGCGTGATCGTCCACTGGTCATGGAGCAGGAGCAGCAGCAGCCGACGCTGCCCAGGTTCGGCCTAGACACCGCCACCATCACGCGCCTCCCATCG[T/C,A]
TCATATATGTCACACCCCAATCTGGCACCGCCGTACAACGGCACCTGACAGGAGCGTGTCGTGGGAAAAACGGCGCGAACCGCTTCCTACGAAACCGTGA
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 39.90% | 0.10% | 8.53% | 51.33% | T: 0.08% |
| All Indica | 2759 | 17.30% | 0.20% | 11.89% | 70.50% | T: 0.11% |
| All Japonica | 1512 | 88.70% | 0.00% | 4.03% | 7.21% | T: 0.07% |
| Aus | 269 | 4.10% | 0.00% | 2.23% | 93.68% | NA |
| Indica I | 595 | 6.70% | 0.20% | 6.72% | 86.39% | NA |
| Indica II | 465 | 11.40% | 0.00% | 6.24% | 82.37% | NA |
| Indica III | 913 | 30.90% | 0.30% | 20.26% | 48.19% | T: 0.33% |
| Indica Intermediate | 786 | 13.10% | 0.10% | 9.41% | 77.35% | NA |
| Temperate Japonica | 767 | 93.00% | 0.00% | 6.52% | 0.39% | T: 0.13% |
| Tropical Japonica | 504 | 78.80% | 0.00% | 1.79% | 19.44% | NA |
| Japonica Intermediate | 241 | 95.90% | 0.00% | 0.83% | 3.32% | NA |
| VI/Aromatic | 96 | 15.60% | 0.00% | 1.04% | 83.33% | NA |
| Intermediate | 90 | 47.80% | 0.00% | 7.78% | 44.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0128509381 | A -> G | LOC_Os01g49570.1 | missense_variant ; p.Phe65Leu; MODERATE | nonsynonymous_codon ; F65L | Average:21.355; most accessible tissue: Zhenshan97 panicle, score: 39.652 | unknown | unknown | TOLERATED | 0.07 |
| vg0128509381 | A -> T | LOC_Os01g49570.1 | missense_variant ; p.Phe65Ile; MODERATE | nonsynonymous_codon ; F65I | Average:21.355; most accessible tissue: Zhenshan97 panicle, score: 39.652 | unknown | unknown | DELETERIOUS | 0.03 |
| vg0128509381 | A -> DEL | LOC_Os01g49570.1 | N | frameshift_variant | Average:21.355; most accessible tissue: Zhenshan97 panicle, score: 39.652 | N | N | N | N |