| Variant ID: vg0131447871 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 31447871 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
ATGAATCCGGCTTCCAGAAGTCGCGCCACCTCCTCGCGGATGAAGGCTTGACGTTCCGGGGCCTGCCGCCGCACTTTCTGCCGGACCGGCCTTGCGCCCG[G/A]
CCGCACGGCGAGACGGTGCTCAATCACCTCCCTGGGGACCCCGGGCATATCCGCCGGTCTCCATGCGAAGACGTCAGCGTTTGCCCGCAGGAAGGAGACG
CGTCTCCTTCCTGCGGGCAAACGCTGACGTCTTCGCATGGAGACCGGCGGATATGCCCGGGGTCCCCAGGGAGGTGATTGAGCACCGTCTCGCCGTGCGG[C/T]
CGGGCGCAAGGCCGGTCCGGCAGAAAGTGCGGCGGCAGGCCCCGGAACGTCAAGCCTTCATCCGCGAGGAGGTGGCGCGACTTCTGGAAGCCGGATTCAT
| 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 | 51.80% | 0.20% | 3.62% | 44.46% | NA |
| All Indica | 2759 | 43.80% | 0.10% | 4.93% | 51.14% | NA |
| All Japonica | 1512 | 68.50% | 0.00% | 1.19% | 30.36% | NA |
| Aus | 269 | 19.70% | 1.50% | 5.58% | 73.23% | NA |
| Indica I | 595 | 30.80% | 0.00% | 4.87% | 64.37% | NA |
| Indica II | 465 | 30.80% | 0.00% | 3.87% | 65.38% | NA |
| Indica III | 913 | 60.50% | 0.10% | 4.93% | 34.50% | NA |
| Indica Intermediate | 786 | 42.10% | 0.30% | 5.60% | 52.04% | NA |
| Temperate Japonica | 767 | 59.80% | 0.00% | 0.65% | 39.50% | NA |
| Tropical Japonica | 504 | 90.70% | 0.00% | 0.40% | 8.93% | NA |
| Japonica Intermediate | 241 | 49.40% | 0.00% | 4.56% | 46.06% | NA |
| VI/Aromatic | 96 | 93.80% | 1.00% | 0.00% | 5.21% | NA |
| Intermediate | 90 | 65.60% | 0.00% | 2.22% | 32.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0131447871 | G -> A | LOC_Os01g54650.1 | downstream_gene_variant ; 4244.0bp to feature; MODIFIER | silent_mutation | Average:26.912; most accessible tissue: Zhenshan97 panicle, score: 59.59 | N | N | N | N |
| vg0131447871 | G -> A | LOC_Os01g54660.1 | intron_variant ; MODIFIER | silent_mutation | Average:26.912; most accessible tissue: Zhenshan97 panicle, score: 59.59 | N | N | N | N |
| vg0131447871 | G -> DEL | N | N | silent_mutation | Average:26.912; most accessible tissue: Zhenshan97 panicle, score: 59.59 | N | N | N | N |