| Variant ID: vg0607893738 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 7893738 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
GAACCATCTCGGGGAAAGCTCATTTCCCCTCCAAAGTGGTCGTTTAACCGACCCCCTCGCAGGTTCGTCTCTCACCCATCGTGGCTGTATTCATTCTCTC[A/G]
ACGCGAGTTTTCACTCACCCATCTTGTTCGTCTTCTGGTCTTTTCTTTTGTTTCAGCGAGATCCCGTCGCGTCCCTCCCGCCATTCCAAGTCCGGCCAGT
ACTGGCCGGACTTGGAATGGCGGGAGGGACGCGACGGGATCTCGCTGAAACAAAAGAAAAGACCAGAAGACGAACAAGATGGGTGAGTGAAAACTCGCGT[T/C]
GAGAGAATGAATACAGCCACGATGGGTGAGAGACGAACCTGCGAGGGGGTCGGTTAAACGACCACTTTGGAGGGGAAATGAGCTTTCCCCGAGATGGTTC
| 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 | 7.00% | 0.50% | 1.65% | 90.82% | NA |
| All Indica | 2759 | 1.00% | 0.80% | 1.20% | 97.03% | NA |
| All Japonica | 1512 | 19.40% | 0.00% | 0.46% | 80.09% | NA |
| Aus | 269 | 0.70% | 0.00% | 12.27% | 86.99% | NA |
| Indica I | 595 | 0.70% | 0.50% | 0.67% | 98.15% | NA |
| Indica II | 465 | 0.40% | 0.40% | 0.43% | 98.71% | NA |
| Indica III | 913 | 1.80% | 1.50% | 1.86% | 94.85% | NA |
| Indica Intermediate | 786 | 0.60% | 0.40% | 1.27% | 97.71% | NA |
| Temperate Japonica | 767 | 34.20% | 0.00% | 0.13% | 65.71% | NA |
| Tropical Japonica | 504 | 2.60% | 0.00% | 0.99% | 96.43% | NA |
| Japonica Intermediate | 241 | 7.90% | 0.00% | 0.41% | 91.70% | NA |
| VI/Aromatic | 96 | 0.00% | 1.00% | 4.17% | 94.79% | NA |
| Intermediate | 90 | 11.10% | 0.00% | 1.11% | 87.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0607893738 | A -> G | LOC_Os06g14140.1 | upstream_gene_variant ; 4000.0bp to feature; MODIFIER | silent_mutation | Average:6.831; most accessible tissue: Callus, score: 21.877 | N | N | N | N |
| vg0607893738 | A -> G | LOC_Os06g14160.1 | downstream_gene_variant ; 2741.0bp to feature; MODIFIER | silent_mutation | Average:6.831; most accessible tissue: Callus, score: 21.877 | N | N | N | N |
| vg0607893738 | A -> G | LOC_Os06g14150.1 | intron_variant ; MODIFIER | silent_mutation | Average:6.831; most accessible tissue: Callus, score: 21.877 | N | N | N | N |
| vg0607893738 | A -> DEL | N | N | silent_mutation | Average:6.831; most accessible tissue: Callus, score: 21.877 | N | N | N | N |