| Variant ID: vg0128724266 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 28724266 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
GTTTGTCTGCTGATGACGTGACCGGCGTCAGACCAGTCACAGACCGGTCATTCTTGTCCACCACGTGTCAGTTTAGCATGTCGCACGTCTGTCCTTCTTC[A/G]
TACAATGACTTCTTTGCAATGGTTGCGATGAAGCCTGGAATGTATCTAGCCGGGACTGGCGTGCTAACTCCAGGAGTTAGCACACCGGCTCCGGCTAGGG
CCCTAGCCGGAGCCGGTGTGCTAACTCCTGGAGTTAGCACGCCAGTCCCGGCTAGATACATTCCAGGCTTCATCGCAACCATTGCAAAGAAGTCATTGTA[T/C]
GAAGAAGGACAGACGTGCGACATGCTAAACTGACACGTGGTGGACAAGAATGACCGGTCTGTGACTGGTCTGACGCCGGTCACGTCATCAGCAGACAAAC
| 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 | 69.00% | 0.20% | 1.93% | 28.86% | NA |
| All Indica | 2759 | 59.80% | 0.00% | 1.81% | 38.35% | NA |
| All Japonica | 1512 | 88.20% | 0.10% | 0.33% | 11.38% | NA |
| Aus | 269 | 62.80% | 0.00% | 13.38% | 23.79% | NA |
| Indica I | 595 | 50.60% | 0.00% | 1.18% | 48.24% | NA |
| Indica II | 465 | 52.00% | 0.00% | 1.08% | 46.88% | NA |
| Indica III | 913 | 70.90% | 0.00% | 1.97% | 27.16% | NA |
| Indica Intermediate | 786 | 58.50% | 0.10% | 2.54% | 38.80% | NA |
| Temperate Japonica | 767 | 99.30% | 0.00% | 0.00% | 0.65% | NA |
| Tropical Japonica | 504 | 68.50% | 0.00% | 0.79% | 30.75% | NA |
| Japonica Intermediate | 241 | 94.20% | 0.40% | 0.41% | 4.98% | NA |
| VI/Aromatic | 96 | 45.80% | 4.20% | 0.00% | 50.00% | NA |
| Intermediate | 90 | 73.30% | 2.20% | 0.00% | 24.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0128724266 | A -> G | LOC_Os01g49990.1 | synonymous_variant ; p.Ser53Ser; LOW | synonymous_codon | Average:13.84; most accessible tissue: Zhenshan97 panicle, score: 24.575 | N | N | N | N |
| vg0128724266 | A -> DEL | LOC_Os01g49990.1 | N | frameshift_variant | Average:13.84; most accessible tissue: Zhenshan97 panicle, score: 24.575 | N | N | N | N |