| Variant ID: vg0424679705 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 24679705 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
TAATATTAGAACACTACACAATCTTATATGATAAGTCTAATTACAGGTCTAATAATCTTAATTAATTGCATTACAAATATAACAATCATTTATATTATTA[T/C]
GTCACTTGTCTGCTCCAATTCCTTCTAGGTCTTCCACTCAGGCTAGCTCTTCCACTCAGGCTTGACGGACGACTCCGACAACACGTCTTTTCTGCAAGAT
ATCTTGCAGAAAAGACGTGTTGTCGGAGTCGTCCGTCAAGCCTGAGTGGAAGAGCTAGCCTGAGTGGAAGACCTAGAAGGAATTGGAGCAGACAAGTGAC[A/G]
TAATAATATAAATGATTGTTATATTTGTAATGCAATTAATTAAGATTATTAGACCTGTAATTAGACTTATCATATAAGATTGTGTAGTGTTCTAATATTA
| 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 | 40.20% | 1.30% | 3.94% | 54.57% | NA |
| All Indica | 2759 | 4.20% | 0.70% | 4.42% | 90.72% | NA |
| All Japonica | 1512 | 98.50% | 0.70% | 0.40% | 0.40% | NA |
| Aus | 269 | 55.00% | 11.20% | 20.07% | 13.75% | NA |
| Indica I | 595 | 4.40% | 0.00% | 0.17% | 95.46% | NA |
| Indica II | 465 | 3.40% | 0.40% | 0.43% | 95.70% | NA |
| Indica III | 913 | 2.20% | 0.90% | 10.19% | 86.75% | NA |
| Indica Intermediate | 786 | 6.90% | 1.00% | 3.31% | 88.80% | NA |
| Temperate Japonica | 767 | 99.50% | 0.00% | 0.26% | 0.26% | NA |
| Tropical Japonica | 504 | 97.20% | 1.40% | 0.79% | 0.60% | NA |
| Japonica Intermediate | 241 | 98.30% | 1.20% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 94.80% | 3.10% | 2.08% | 0.00% | NA |
| Intermediate | 90 | 60.00% | 1.10% | 2.22% | 36.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0424679705 | T -> C | LOC_Os04g41599.1 | intron_variant ; MODIFIER | silent_mutation | Average:7.201; most accessible tissue: Callus, score: 22.426 | N | N | N | N |
| vg0424679705 | T -> DEL | N | N | silent_mutation | Average:7.201; most accessible tissue: Callus, score: 22.426 | N | N | N | N |