| Variant ID: vg0319758726 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 19758726 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TATCAGACACTCTACCTCCATTAGCTAAAAGATGCTCTGTCAACTGTGGCGCACCTCGGAAGGTATTTCTTCTCTGACGTTTTGTCATTCCTGGTGGAGG[C/T]
CATTCTGTGCTGGTAATGCTCATCTTACGGACTTCATCTTCGGTTCGCATTGGTGTTTTTTTTTTCTGCTGAGGACACTCCCTTGCATAGTGCCCTTGCT
AGCAAGGGCACTATGCAAGGGAGTGTCCTCAGCAGAAAAAAAAAACACCAATGCGAACCGAAGATGAAGTCCGTAAGATGAGCATTACCAGCACAGAATG[G/A]
CCTCCACCAGGAATGACAAAACGTCAGAGAAGAAATACCTTCCGAGGTGCGCCACAGTTGACAGAGCATCTTTTAGCTAATGGAGGTAGAGTGTCTGATA
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 28.00% | 4.60% | 15.21% | 52.18% | NA |
| All Indica | 2759 | 2.80% | 0.30% | 22.07% | 74.85% | NA |
| All Japonica | 1512 | 71.90% | 13.70% | 4.10% | 10.32% | NA |
| Aus | 269 | 13.80% | 0.00% | 10.78% | 75.46% | NA |
| Indica I | 595 | 1.70% | 0.20% | 14.96% | 83.19% | NA |
| Indica II | 465 | 3.90% | 0.00% | 18.49% | 77.63% | NA |
| Indica III | 913 | 1.80% | 0.20% | 29.24% | 68.78% | NA |
| Indica Intermediate | 786 | 4.20% | 0.60% | 21.25% | 73.92% | NA |
| Temperate Japonica | 767 | 96.00% | 2.90% | 0.91% | 0.26% | NA |
| Tropical Japonica | 504 | 34.70% | 30.40% | 7.94% | 26.98% | NA |
| Japonica Intermediate | 241 | 73.00% | 13.30% | 6.22% | 7.47% | NA |
| VI/Aromatic | 96 | 83.30% | 0.00% | 2.08% | 14.58% | NA |
| Intermediate | 90 | 47.80% | 2.20% | 18.89% | 31.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0319758726 | C -> T | LOC_Os03g35670.1 | N | stop_gained | Average:6.031; most accessible tissue: Callus, score: 18.7 | N | N | N | N |
| vg0319758726 | C -> DEL | LOC_Os03g35670.1 | N | frameshift_variant | Average:6.031; most accessible tissue: Callus, score: 18.7 | N | N | N | N |