| Variant ID: vg0710350287 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 10350287 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CCTCAGGATCCTGCACCGTCTCCTCCTCATGCTCCCCCAGCACCGTCTCCACCTCAGGCTCCAGCATCGACTCCTCCTCAGGATCCTGCACCGACTCCTC[C/A]
TCGTGCTCCTACACCTACTCCCCCGCAAGCTCCTCTTTCGGCACCTTCAAAGTCAAGGGCCCCCCAGCTCCACCGCCTGCCCACACAAGGGCAACGAAGA
TCTTCGTTGCCCTTGTGTGGGCAGGCGGTGGAGCTGGGGGGCCCTTGACTTTGAAGGTGCCGAAAGAGGAGCTTGCGGGGGAGTAGGTGTAGGAGCACGA[G/T]
GAGGAGTCGGTGCAGGATCCTGAGGAGGAGTCGATGCTGGAGCCTGAGGTGGAGACGGTGCTGGGGGAGCATGAGGAGGAGACGGTGCAGGATCCTGAGG
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 30.60% | 0.30% | 5.42% | 63.65% | NA |
| All Indica | 2759 | 5.10% | 0.00% | 3.30% | 91.59% | NA |
| All Japonica | 1512 | 74.50% | 1.00% | 9.99% | 14.48% | NA |
| Aus | 269 | 51.30% | 0.00% | 4.46% | 44.24% | NA |
| Indica I | 595 | 7.90% | 0.00% | 1.51% | 90.59% | NA |
| Indica II | 465 | 6.90% | 0.00% | 1.51% | 91.61% | NA |
| Indica III | 913 | 1.30% | 0.00% | 1.53% | 97.15% | NA |
| Indica Intermediate | 786 | 6.40% | 0.00% | 7.76% | 85.88% | NA |
| Temperate Japonica | 767 | 61.70% | 0.00% | 14.34% | 23.99% | NA |
| Tropical Japonica | 504 | 90.10% | 3.00% | 2.18% | 4.76% | NA |
| Japonica Intermediate | 241 | 83.00% | 0.00% | 12.45% | 4.56% | NA |
| VI/Aromatic | 96 | 2.10% | 0.00% | 1.04% | 96.88% | NA |
| Intermediate | 90 | 43.30% | 0.00% | 1.11% | 55.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0710350287 | C -> DEL | LOC_Os07g17510.1 | N | frameshift_variant | Average:5.806; most accessible tissue: Callus, score: 10.028 | N | N | N | N |
| vg0710350287 | C -> A | LOC_Os07g17510.1 | synonymous_variant ; p.Ser553Ser; LOW | synonymous_codon | Average:5.806; most accessible tissue: Callus, score: 10.028 | N | N | N | N |