| Variant ID: vg0143002027 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 43002027 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
CGACGGTGGCAATGGTGGCCCCAGGCTCTTGGAAACCTAGGTCATCATCGCCGTCATCGATGTCCTCGGCGGGGGCCTTCTGCTTGGCCTCACTTCGCCG[A/G]
TTGCCGGAAGGAACCGCCGGGGACTTGCCCTCTCGGCGCTCCTGCCTCCTCTCCTCCTCCTACTTCCTCGTCCGCTCAGCCAAACTTTTGACTGCGCGGC
GCCGCGCAGTCAAAAGTTTGGCTGAGCGGACGAGGAAGTAGGAGGAGGAGAGGAGGCAGGAGCGCCGAGAGGGCAAGTCCCCGGCGGTTCCTTCCGGCAA[T/C]
CGGCGAAGTGAGGCCAAGCAGAAGGCCCCCGCCGAGGACATCGATGACGGCGATGATGACCTAGGTTTCCAAGAGCCTGGGGCCACCATTGCCACCGTCG
| 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 | 9.10% | 0.60% | 7.62% | 82.71% | NA |
| All Indica | 2759 | 3.40% | 0.00% | 6.13% | 90.47% | NA |
| All Japonica | 1512 | 21.00% | 1.70% | 8.27% | 69.05% | NA |
| Aus | 269 | 1.10% | 0.00% | 8.18% | 90.71% | NA |
| Indica I | 595 | 0.50% | 0.00% | 2.18% | 97.31% | NA |
| Indica II | 465 | 1.90% | 0.00% | 2.80% | 95.27% | NA |
| Indica III | 913 | 6.50% | 0.10% | 10.30% | 83.13% | NA |
| Indica Intermediate | 786 | 2.80% | 0.00% | 6.23% | 90.97% | NA |
| Temperate Japonica | 767 | 38.70% | 0.10% | 4.69% | 56.45% | NA |
| Tropical Japonica | 504 | 2.00% | 4.60% | 12.10% | 81.35% | NA |
| Japonica Intermediate | 241 | 4.10% | 0.80% | 11.62% | 83.40% | NA |
| VI/Aromatic | 96 | 3.10% | 0.00% | 31.25% | 65.62% | NA |
| Intermediate | 90 | 15.60% | 0.00% | 15.56% | 68.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0143002027 | A -> G | LOC_Os01g74240.1 | downstream_gene_variant ; 4544.0bp to feature; MODIFIER | silent_mutation | Average:6.048; most accessible tissue: Callus, score: 12.637 | N | N | N | N |
| vg0143002027 | A -> G | LOC_Os01g74230.1 | intron_variant ; MODIFIER | silent_mutation | Average:6.048; most accessible tissue: Callus, score: 12.637 | N | N | N | N |
| vg0143002027 | A -> DEL | N | N | silent_mutation | Average:6.048; most accessible tissue: Callus, score: 12.637 | N | N | N | N |