| Variant ID: vg0320572124 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 20572124 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CTGAAATCATCCCTCAAGGGCCGTATCTATCGTTTCTGACATGTTATCTTAAATAATCATTCAAAGATTTCAAGATGTATTAGATGTATCACTCCGACGA[A/T]
CATACAAGTCAACTTCTATTAGTTATAACAAAAATGATTTGATAAATATAATTGCCAATGTATATATGTATCTGTCTGTCAATGCAAATAGTGTATTATA
TATAATACACTATTTGCATTGACAGACAGATACATATATACATTGGCAATTATATTTATCAAATCATTTTTGTTATAACTAATAGAAGTTGACTTGTATG[T/A]
TCGTCGGAGTGATACATCTAATACATCTTGAAATCTTTGAATGATTATTTAAGATAACATGTCAGAAACGATAGATACGGCCCTTGAGGGATGATTTCAG
| 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 | 98.30% | 1.50% | 0.19% | 0.00% | NA |
| All Indica | 2759 | 97.20% | 2.50% | 0.33% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 98.20% | 1.30% | 0.50% | 0.00% | NA |
| Indica II | 465 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica III | 913 | 95.20% | 4.70% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 97.20% | 2.20% | 0.64% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 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 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 100.00% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0320572124 | A -> T | LOC_Os03g37110.1 | upstream_gene_variant ; 3601.0bp to feature; MODIFIER | silent_mutation | Average:74.792; most accessible tissue: Zhenshan97 panicle, score: 87.451 | N | N | N | N |
| vg0320572124 | A -> T | LOC_Os03g37130.1 | downstream_gene_variant ; 2117.0bp to feature; MODIFIER | silent_mutation | Average:74.792; most accessible tissue: Zhenshan97 panicle, score: 87.451 | N | N | N | N |
| vg0320572124 | A -> T | LOC_Os03g37120.1 | intron_variant ; MODIFIER | silent_mutation | Average:74.792; most accessible tissue: Zhenshan97 panicle, score: 87.451 | N | N | N | N |