| Variant ID: vg0627802083 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 27802083 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 259. )
CATCCTTTCAGAATGTTATGTATGTTGATACCGATGGCCAGCCCTATCCTCCTCCTGTTTGGCCTGCTGGTCTCGAAGTTTATGCAAGCAATACGAAATG[C/A]
TACCAAGCTAGCATTTTTGAGGATAACATGTTTTACTATGTGGGGCCAGGTAGTTGTACTAGTTAAAATTAGAATCTCTTGAAAATATTAATGGCGAGGG
CCCTCGCCATTAATATTTTCAAGAGATTCTAATTTTAACTAGTACAACTACCTGGCCCCACATAGTAAAACATGTTATCCTCAAAAATGCTAGCTTGGTA[G/T]
CATTTCGTATTGCTTGCATAAACTTCGAGACCAGCAGGCCAAACAGGAGGAGGATAGGGCTGGCCATCGGTATCAACATACATAACATTCTGAAAGGATG
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.80% | 0.10% | 0.04% | 0.00% | NA |
| All Indica | 2759 | 99.90% | 0.00% | 0.07% | 0.00% | NA |
| All Japonica | 1512 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Aus | 269 | 98.50% | 1.50% | 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 | 99.70% | 0.00% | 0.25% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.20% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0627802083 | C -> A | LOC_Os06g45920.1 | stop_gained ; p.Cys217*; HIGH | N | Average:70.997; most accessible tissue: Zhenshan97 panicle, score: 82.336 | N | N | N | N |
| vg0627802083 | C -> A | LOC_Os06g45910.1 | downstream_gene_variant ; 3503.0bp to feature; MODIFIER | N | Average:70.997; most accessible tissue: Zhenshan97 panicle, score: 82.336 | N | N | N | N |