| Variant ID: vg0121350314 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 21350314 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TCCCTCTGTTTTTTCTCTATTTGACATTGAACTAACCAACATCAGAAGTTTGGAAACATAGACATTATTAATTATTTGCTACATTTCATTCATCTAAAAA[T/A]
TTTTAATTTTGAAATCACCTAAAACTACATGCTTCTAAACAGGGAGGAACGTAGCATCAAACTAGAAGTGCTCATCTTTTTCTTCATCTTTTGGCTCCCT
AGGGAGCCAAAAGATGAAGAAAAAGATGAGCACTTCTAGTTTGATGCTACGTTCCTCCCTGTTTAGAAGCATGTAGTTTTAGGTGATTTCAAAATTAAAA[A/T]
TTTTTAGATGAATGAAATGTAGCAAATAATTAATAATGTCTATGTTTCCAAACTTCTGATGTTGGTTAGTTCAATGTCAAATAGAGAAAAAACAGAGGGA
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 98.60% | 1.30% | 0.02% | 0.00% | NA |
| All Indica | 2759 | 98.90% | 1.10% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 98.10% | 1.90% | 0.07% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 96.20% | 3.80% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 96.20% | 3.70% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 97.90% | 2.10% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 97.80% | 2.20% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0121350314 | T -> A | LOC_Os01g38120.1 | upstream_gene_variant ; 640.0bp to feature; MODIFIER | silent_mutation | Average:54.318; most accessible tissue: Callus, score: 80.173 | N | N | N | N |
| vg0121350314 | T -> A | LOC_Os01g38140.1 | upstream_gene_variant ; 4156.0bp to feature; MODIFIER | silent_mutation | Average:54.318; most accessible tissue: Callus, score: 80.173 | N | N | N | N |
| vg0121350314 | T -> A | LOC_Os01g38130.1 | intron_variant ; MODIFIER | silent_mutation | Average:54.318; most accessible tissue: Callus, score: 80.173 | N | N | N | N |