| Variant ID: vg0721995082 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 21995082 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
ATGTGGATGACAAAGAAGCATAAGAGACATAATTGGCTATGTTATTCTCATCATCATTCACACCTTGAGCTTCAAAACCATACCTTTGTGGAGGTTTACC[T/C]
GCATTGCTTCTTACCCCCATTCTTATAACAATAGGAAGATTAGTTTCTTCTCCCCCTGTTTCAAACTCCTCTCCTTCCGTATCCGATGAAATCTGTATAG
CTATACAGATTTCATCGGATACGGAAGGAGAGGAGTTTGAAACAGGGGGAGAAGAAACTAATCTTCCTATTGTTATAAGAATGGGGGTAAGAAGCAATGC[A/G]
GGTAAACCTCCACAAAGGTATGGTTTTGAAGCTCAAGGTGTGAATGATGATGAGAATAACATAGCCAATTATGTCTCTTATGCTTCTTTGTCATCCACAT
| 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 | 35.80% | 0.80% | 33.14% | 30.24% | NA |
| All Indica | 2759 | 14.00% | 0.00% | 45.78% | 40.27% | NA |
| All Japonica | 1512 | 81.30% | 2.20% | 6.68% | 9.79% | NA |
| Aus | 269 | 0.70% | 0.00% | 46.47% | 52.79% | NA |
| Indica I | 595 | 5.50% | 0.00% | 24.03% | 70.42% | NA |
| Indica II | 465 | 20.40% | 0.00% | 49.46% | 30.11% | NA |
| Indica III | 913 | 13.80% | 0.00% | 58.71% | 27.49% | NA |
| Indica Intermediate | 786 | 16.70% | 0.00% | 45.04% | 38.30% | NA |
| Temperate Japonica | 767 | 94.30% | 0.00% | 1.69% | 4.04% | NA |
| Tropical Japonica | 504 | 68.10% | 6.50% | 12.90% | 12.50% | NA |
| Japonica Intermediate | 241 | 67.60% | 0.40% | 9.54% | 22.41% | NA |
| VI/Aromatic | 96 | 35.40% | 3.10% | 51.04% | 10.42% | NA |
| Intermediate | 90 | 48.90% | 0.00% | 31.11% | 20.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0721995082 | T -> DEL | LOC_Os07g36710.1 | N | frameshift_variant | Average:5.426; most accessible tissue: Callus, score: 15.021 | N | N | N | N |
| vg0721995082 | T -> C | LOC_Os07g36710.1 | synonymous_variant ; p.Ala247Ala; LOW | synonymous_codon | Average:5.426; most accessible tissue: Callus, score: 15.021 | N | N | N | N |