| Variant ID: vg0143002039 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 43002039 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TGGTGGCCCCAGGCTCTTGGAAACCTAGGTCATCATCGCCGTCATCGATGTCCTCGGCGGGGGCCTTCTGCTTGGCCTCACTTCGCCGATTGCCGGAAGG[A/T]
ACCGCCGGGGACTTGCCCTCTCGGCGCTCCTGCCTCCTCTCCTCCTCCTACTTCCTCGTCCGCTCAGCCAAACTTTTGACTGCGCGGCAGTCCGCGAGGT
ACCTCGCGGACTGCCGCGCAGTCAAAAGTTTGGCTGAGCGGACGAGGAAGTAGGAGGAGGAGAGGAGGCAGGAGCGCCGAGAGGGCAAGTCCCCGGCGGT[T/A]
CCTTCCGGCAATCGGCGAAGTGAGGCCAAGCAGAAGGCCCCCGCCGAGGACATCGATGACGGCGATGATGACCTAGGTTTCCAAGAGCCTGGGGCCACCA
| Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 8.80% | 0.50% | 5.76% | 84.93% | NA |
| All Indica | 2759 | 1.00% | 0.70% | 5.00% | 93.26% | NA |
| All Japonica | 1512 | 24.70% | 0.00% | 4.96% | 70.30% | NA |
| Aus | 269 | 0.70% | 0.00% | 18.59% | 80.67% | NA |
| Indica I | 595 | 0.50% | 0.00% | 1.34% | 98.15% | NA |
| Indica II | 465 | 1.30% | 0.00% | 3.66% | 95.05% | NA |
| Indica III | 913 | 0.70% | 1.90% | 8.21% | 89.27% | NA |
| Indica Intermediate | 786 | 1.70% | 0.40% | 4.83% | 93.13% | NA |
| Temperate Japonica | 767 | 39.40% | 0.00% | 2.09% | 58.54% | NA |
| Tropical Japonica | 504 | 11.70% | 0.00% | 8.53% | 79.76% | NA |
| Japonica Intermediate | 241 | 5.40% | 0.00% | 6.64% | 87.97% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 4.17% | 95.83% | NA |
| Intermediate | 90 | 15.60% | 2.20% | 5.56% | 76.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0143002039 | A -> T | LOC_Os01g74240.1 | downstream_gene_variant ; 4532.0bp to feature; MODIFIER | silent_mutation | Average:6.048; most accessible tissue: Callus, score: 12.637 | N | N | N | N |
| vg0143002039 | A -> T | LOC_Os01g74230.1 | intron_variant ; MODIFIER | silent_mutation | Average:6.048; most accessible tissue: Callus, score: 12.637 | N | N | N | N |
| vg0143002039 | A -> DEL | N | N | silent_mutation | Average:6.048; most accessible tissue: Callus, score: 12.637 | N | N | N | N |