| Variant ID: vg0320569919 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 20569919 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CGTCCCAAGATTCACCTCCGCCAGTGGCGTCCCCGTCAGTATCCTCACCTCCTCCGGCACCGACGACACCGCCCTCTCCGCCCCCACCAAGCAAGTCCCC[T/A]
CCACCGCCGTCTCCGCCTCCTACTACGTCGTCGACACCGCCATCGCATCAATCACCTCCGGAAGAAGGAACCTCGCCGCCACCTTCGCCATCATCAGGGG
CCCCTGATGATGGCGAAGGTGGCGGCGAGGTTCCTTCTTCCGGAGGTGATTGATGCGATGGCGGTGTCGACGACGTAGTAGGAGGCGGAGACGGCGGTGG[A/T]
GGGGACTTGCTTGGTGGGGGCGGAGAGGGCGGTGTCGTCGGTGCCGGAGGAGGTGAGGATACTGACGGGGACGCCACTGGCGGAGGTGAATCTTGGGACG
| 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 | 99.50% | 0.30% | 0.19% | 0.00% | NA |
| All Indica | 2759 | 99.70% | 0.20% | 0.04% | 0.00% | NA |
| All Japonica | 1512 | 98.90% | 0.60% | 0.53% | 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 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.40% | 0.50% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 99.10% | 0.40% | 0.52% | 0.00% | NA |
| Tropical Japonica | 504 | 98.60% | 1.00% | 0.40% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.80% | 0.40% | 0.83% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0320569919 | T -> A | LOC_Os03g37120.1 | synonymous_variant ; p.Pro109Pro; LOW | N | Average:76.747; most accessible tissue: Zhenshan97 panicle, score: 88.35 | N | N | N | N |
| vg0320569919 | T -> A | LOC_Os03g37110.1 | upstream_gene_variant ; 1396.0bp to feature; MODIFIER | N | Average:76.747; most accessible tissue: Zhenshan97 panicle, score: 88.35 | N | N | N | N |
| vg0320569919 | T -> A | LOC_Os03g37100.1 | downstream_gene_variant ; 4853.0bp to feature; MODIFIER | N | Average:76.747; most accessible tissue: Zhenshan97 panicle, score: 88.35 | N | N | N | N |
| vg0320569919 | T -> A | LOC_Os03g37130.1 | downstream_gene_variant ; 4322.0bp to feature; MODIFIER | N | Average:76.747; most accessible tissue: Zhenshan97 panicle, score: 88.35 | N | N | N | N |