| Variant ID: vg0607893739 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 7893739 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
AACCATCTCGGGGAAAGCTCATTTCCCCTCCAAAGTGGTCGTTTAACCGACCCCCTCGCAGGTTCGTCTCTCACCCATCGTGGCTGTATTCATTCTCTCA[A/G]
CGCGAGTTTTCACTCACCCATCTTGTTCGTCTTCTGGTCTTTTCTTTTGTTTCAGCGAGATCCCGTCGCGTCCCTCCCGCCATTCCAAGTCCGGCCAGTC
GACTGGCCGGACTTGGAATGGCGGGAGGGACGCGACGGGATCTCGCTGAAACAAAAGAAAAGACCAGAAGACGAACAAGATGGGTGAGTGAAAACTCGCG[T/C]
TGAGAGAATGAATACAGCCACGATGGGTGAGAGACGAACCTGCGAGGGGGTCGGTTAAACGACCACTTTGGAGGGGAAATGAGCTTTCCCCGAGATGGTT
| 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 | 12.70% | 0.20% | 12.59% | 74.44% | NA |
| All Indica | 2759 | 8.10% | 0.40% | 17.76% | 73.72% | NA |
| All Japonica | 1512 | 20.00% | 0.00% | 1.59% | 78.37% | NA |
| Aus | 269 | 19.30% | 0.00% | 20.45% | 60.22% | NA |
| Indica I | 595 | 2.40% | 0.30% | 10.08% | 87.23% | NA |
| Indica II | 465 | 8.00% | 0.00% | 11.61% | 80.43% | NA |
| Indica III | 913 | 12.30% | 1.00% | 24.97% | 61.77% | NA |
| Indica Intermediate | 786 | 7.80% | 0.00% | 18.83% | 73.41% | NA |
| Temperate Japonica | 767 | 34.30% | 0.00% | 0.26% | 65.45% | NA |
| Tropical Japonica | 504 | 3.60% | 0.00% | 3.17% | 93.25% | NA |
| Japonica Intermediate | 241 | 9.10% | 0.00% | 2.49% | 88.38% | NA |
| VI/Aromatic | 96 | 5.20% | 0.00% | 18.75% | 76.04% | NA |
| Intermediate | 90 | 20.00% | 0.00% | 8.89% | 71.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0607893739 | A -> G | LOC_Os06g14140.1 | upstream_gene_variant ; 4001.0bp to feature; MODIFIER | silent_mutation | Average:6.831; most accessible tissue: Callus, score: 21.877 | N | N | N | N |
| vg0607893739 | A -> G | LOC_Os06g14160.1 | downstream_gene_variant ; 2740.0bp to feature; MODIFIER | silent_mutation | Average:6.831; most accessible tissue: Callus, score: 21.877 | N | N | N | N |
| vg0607893739 | A -> G | LOC_Os06g14150.1 | intron_variant ; MODIFIER | silent_mutation | Average:6.831; most accessible tissue: Callus, score: 21.877 | N | N | N | N |
| vg0607893739 | A -> DEL | N | N | silent_mutation | Average:6.831; most accessible tissue: Callus, score: 21.877 | N | N | N | N |