| Variant ID: vg0135353033 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 35353033 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CCCATCCTTGGATTGCCCTGTAAAAATAGTAATGTTATTCAGTTTGGGTAGTAATTTTGTGCAAATCATAGCGGATTTTGTAAATGGTTAGACATACAAC[G/A]
AAATCGTTGTCTACATTGGGGCAGACAAAATATCTCCTTCGAAATGTTTGTTCAACAAAGGATGTAGCCACCTGCCAGCGATCTCTGCACCCACACTTTG
CAAAGTGTGGGTGCAGAGATCGCTGGCAGGTGGCTACATCCTTTGTTGAACAAACATTTCGAAGGAGATATTTTGTCTGCCCCAATGTAGACAACGATTT[C/T]
GTTGTATGTCTAACCATTTACAAAATCCGCTATGATTTGCACAAAATTACTACCCAAACTGAATAACATTACTATTTTTACAGGGCAATCCAAGGATGGG
| 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 | 23.80% | 0.20% | 2.98% | 72.98% | NA |
| All Indica | 2759 | 2.20% | 0.00% | 2.07% | 95.72% | NA |
| All Japonica | 1512 | 61.60% | 0.70% | 3.57% | 34.13% | NA |
| Aus | 269 | 0.70% | 0.00% | 9.29% | 89.96% | NA |
| Indica I | 595 | 3.90% | 0.00% | 0.34% | 95.80% | NA |
| Indica II | 465 | 0.40% | 0.00% | 2.58% | 96.99% | NA |
| Indica III | 913 | 0.40% | 0.00% | 2.96% | 96.60% | NA |
| Indica Intermediate | 786 | 4.10% | 0.00% | 2.04% | 93.89% | NA |
| Temperate Japonica | 767 | 55.40% | 0.00% | 1.69% | 42.89% | NA |
| Tropical Japonica | 504 | 61.30% | 2.20% | 7.34% | 29.17% | NA |
| Japonica Intermediate | 241 | 81.70% | 0.00% | 1.66% | 16.60% | NA |
| VI/Aromatic | 96 | 92.70% | 0.00% | 0.00% | 7.29% | NA |
| Intermediate | 90 | 46.70% | 0.00% | 5.56% | 47.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0135353033 | G -> A | LOC_Os01g61080.1 | downstream_gene_variant ; 2388.0bp to feature; MODIFIER | silent_mutation | Average:17.275; most accessible tissue: Zhenshan97 root, score: 39.742 | N | N | N | N |
| vg0135353033 | G -> A | LOC_Os01g61090.1 | intron_variant ; MODIFIER | silent_mutation | Average:17.275; most accessible tissue: Zhenshan97 root, score: 39.742 | N | N | N | N |
| vg0135353033 | G -> DEL | N | N | silent_mutation | Average:17.275; most accessible tissue: Zhenshan97 root, score: 39.742 | N | N | N | N |