| Variant ID: vg0302709043 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 2709043 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.98, C: 0.03, others allele: 0.00, population size: 286. )
ACAAAGGTCAGCTTAATGACGGCACTCTTATCGCCGTCAAACGGGCCAAGAAGGTTTGCTCTTATTTCTTAATGTTCATTTTGCAGACTGCATTAGCTAT[T/C]
GAATACTGATTACCTTGGTCGCCTTTCTTTGCAGAATGTGTACGACAAGCATATGGGTCGTGAGTTCCGGAACGAGATTGAGACGTTGCAATGTATCGAG
CTCGATACATTGCAACGTCTCAATCTCGTTCCGGAACTCACGACCCATATGCTTGTCGTACACATTCTGCAAAGAAAGGCGACCAAGGTAATCAGTATTC[A/G]
ATAGCTAATGCAGTCTGCAAAATGAACATTAAGAAATAAGAGCAAACCTTCTTGGCCCGTTTGACGGCGATAAGAGTGCCGTCATTAAGCTGACCTTTGT
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.50% | 0.50% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 99.50% | 0.50% | 0.00% | 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 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.30% | 1.70% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 86.50% | 13.50% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 96.70% | 3.30% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0302709043 | T -> C | LOC_Os03g05480.1 | downstream_gene_variant ; 4270.0bp to feature; MODIFIER | silent_mutation | Average:71.06; most accessible tissue: Callus, score: 85.954 | N | N | N | N |
| vg0302709043 | T -> C | LOC_Os03g05470.1 | intron_variant ; MODIFIER | silent_mutation | Average:71.06; most accessible tissue: Callus, score: 85.954 | N | N | N | N |