| Variant ID: vg0204160056 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 4160056 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
GCCATTATTTCCAGGCGCATCGGGTCACGGTGGTTACGTCTTATCCCCTCGGCCAAATCTTGTATAACCGAGAGGGTACTGGACGGGTGGTGAAATGGGC[A/G]
ATCGAACTCTCTGAATTCGATTTGCGCTTTGAACCAAGCCACGCGATCAAGAGCCAGGCCCTCGCCGACTTTGTGGTGGAGTGGACCCCAGCTCCCGAGC
GCTCGGGAGCTGGGGTCCACTCCACCACAAAGTCGGCGAGGGCCTGGCTCTTGATCGCGTGGCTTGGTTCAAAGCGCAAATCGAATTCAGAGAGTTCGAT[T/C]
GCCCATTTCACCACCCGTCCAGTACCCTCTCGGTTATACAAGATTTGGCCGAGGGGATAAGACGTAACCACCGTGACCCGATGCGCCTGGAAATAATGGC
| 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 | 80.40% | 0.40% | 5.46% | 13.73% | NA |
| All Indica | 2759 | 75.40% | 0.70% | 6.02% | 17.94% | NA |
| All Japonica | 1512 | 92.50% | 0.00% | 5.29% | 2.25% | NA |
| Aus | 269 | 54.30% | 0.00% | 2.60% | 43.12% | NA |
| Indica I | 595 | 97.30% | 0.00% | 1.01% | 1.68% | NA |
| Indica II | 465 | 79.10% | 0.00% | 3.44% | 17.42% | NA |
| Indica III | 913 | 59.70% | 1.50% | 9.42% | 29.35% | NA |
| Indica Intermediate | 786 | 74.80% | 0.50% | 7.38% | 17.30% | NA |
| Temperate Japonica | 767 | 88.80% | 0.00% | 7.17% | 4.04% | NA |
| Tropical Japonica | 504 | 96.40% | 0.00% | 2.98% | 0.60% | NA |
| Japonica Intermediate | 241 | 95.90% | 0.00% | 4.15% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 88.90% | 1.10% | 5.56% | 4.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0204160056 | A -> G | LOC_Os02g07950.1 | synonymous_variant ; p.Ala172Ala; LOW | synonymous_codon | Average:48.653; most accessible tissue: Zhenshan97 panicle, score: 71.253 | N | N | N | N |
| vg0204160056 | A -> DEL | LOC_Os02g07950.1 | N | frameshift_variant | Average:48.653; most accessible tissue: Zhenshan97 panicle, score: 71.253 | N | N | N | N |