| Variant ID: vg0420971154 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 20971154 |
| Reference Allele: T | Alternative Allele: G |
| Primary Allele: T | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
ACCCAGTTCAGTTGCCTGCAACTGTAATTTCATCTACTGCTCAGAAGTTAGGGTAAGATCTCTCTCTCTCTGTTCTATACATACTCTGGATGTAAGGTTT[T/G]
ACAACATTCTAAATAATACTAATGTATCCATTAGGTACGGTACTAGTTTGTTCAAGAGATTTCAGGCTGCGGGTTTTCCTGTGCAAATGCTCAAAATTCA
TGAATTTTGAGCATTTGCACAGGAAAACCCGCAGCCTGAAATCTCTTGAACAAACTAGTACCGTACCTAATGGATACATTAGTATTATTTAGAATGTTGT[A/C]
AAACCTTACATCCAGAGTATGTATAGAACAGAGAGAGAGAGATCTTACCCTAACTTCTGAGCAGTAGATGAAATTACAGTTGCAGGCAACTGAACTGGGT
| Populations | Population Size | Frequency of T(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 66.30% | 0.90% | 1.78% | 31.08% | NA |
| All Indica | 2759 | 46.60% | 0.20% | 0.62% | 52.59% | NA |
| All Japonica | 1512 | 93.30% | 2.40% | 4.10% | 0.20% | NA |
| Aus | 269 | 98.50% | 0.00% | 0.00% | 1.49% | NA |
| Indica I | 595 | 77.60% | 0.00% | 0.50% | 21.85% | NA |
| Indica II | 465 | 20.00% | 0.60% | 0.65% | 78.71% | NA |
| Indica III | 913 | 45.60% | 0.00% | 0.55% | 53.89% | NA |
| Indica Intermediate | 786 | 40.10% | 0.30% | 0.76% | 58.91% | NA |
| Temperate Japonica | 767 | 99.90% | 0.00% | 0.00% | 0.13% | NA |
| Tropical Japonica | 504 | 83.30% | 5.80% | 10.52% | 0.40% | NA |
| Japonica Intermediate | 241 | 93.40% | 2.90% | 3.73% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 0.00% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 83.30% | 0.00% | 4.44% | 12.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0420971154 | T -> DEL | N | N | silent_mutation | Average:15.52; most accessible tissue: Zhenshan97 root, score: 50.453 | N | N | N | N |
| vg0420971154 | T -> G | LOC_Os04g34670.1 | intron_variant ; MODIFIER | silent_mutation | Average:15.52; most accessible tissue: Zhenshan97 root, score: 50.453 | N | N | N | N |