| Variant ID: vg0424679714 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 24679714 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
AACACTACACAATCTTATATGATAAGTCTAATTACAGGTCTAATAATCTTAATTAATTGCATTACAAATATAACAATCATTTATATTATTATGTCACTTG[T/C]
CTGCTCCAATTCCTTCTAGGTCTTCCACTCAGGCTAGCTCTTCCACTCAGGCTTGACGGACGACTCCGACAACACGTCTTTTCTGCAAGATAAAAAAAAT
ATTTTTTTTATCTTGCAGAAAAGACGTGTTGTCGGAGTCGTCCGTCAAGCCTGAGTGGAAGAGCTAGCCTGAGTGGAAGACCTAGAAGGAATTGGAGCAG[A/G]
CAAGTGACATAATAATATAAATGATTGTTATATTTGTAATGCAATTAATTAAGATTATTAGACCTGTAATTAGACTTATCATATAAGATTGTGTAGTGTT
| 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% | 2.75% | 55.76% | NA |
| All Indica | 2759 | 4.20% | 0.70% | 2.43% | 92.68% | NA |
| All Japonica | 1512 | 98.70% | 0.50% | 0.46% | 0.40% | NA |
| Aus | 269 | 55.00% | 11.50% | 19.70% | 13.75% | NA |
| Indica I | 595 | 4.50% | 0.00% | 0.17% | 95.29% | NA |
| Indica II | 465 | 3.40% | 0.40% | 0.00% | 96.13% | NA |
| Indica III | 913 | 2.20% | 0.90% | 4.71% | 92.22% | NA |
| Indica Intermediate | 786 | 6.90% | 1.00% | 2.93% | 89.19% | NA |
| Temperate Japonica | 767 | 99.50% | 0.00% | 0.26% | 0.26% | NA |
| Tropical Japonica | 504 | 97.60% | 0.80% | 0.99% | 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 | 58.90% | 1.10% | 1.11% | 38.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0424679714 | T -> C | LOC_Os04g41599.1 | intron_variant ; MODIFIER | silent_mutation | Average:7.201; most accessible tissue: Callus, score: 22.426 | N | N | N | N |
| vg0424679714 | T -> DEL | N | N | silent_mutation | Average:7.201; most accessible tissue: Callus, score: 22.426 | N | N | N | N |