| Variant ID: vg0136521761 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 36521761 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GTGGTGACAAACTAATTTTCCTGTGACCCTGCGGCAAAGAAGAAAATTTTAGGCAACGTGTCTTGATCTTGCCGTACAAAAATAAACGAATACTAACCTG[C/T]
TGCTTTGGATGAAATCCACTGCTATGGCCCATCGATTTTGCCATTGTTGCCCCGCTCCTGCATTCAGCCGACTCTAGATCGATTACTTCTGCTTCAGGAA
TTCCTGAAGCAGAAGTAATCGATCTAGAGTCGGCTGAATGCAGGAGCGGGGCAACAATGGCAAAATCGATGGGCCATAGCAGTGGATTTCATCCAAAGCA[G/A]
CAGGTTAGTATTCGTTTATTTTTGTACGGCAAGATCAAGACACGTTGCCTAAAATTTTCTTCTTTGCCGCAGGGTCACAGGAAAATTAGTTTGTCACCAC
| 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 | 38.20% | 1.70% | 10.18% | 50.00% | NA |
| All Indica | 2759 | 5.50% | 2.80% | 12.54% | 79.09% | NA |
| All Japonica | 1512 | 98.30% | 0.00% | 0.13% | 1.59% | NA |
| Aus | 269 | 5.90% | 0.00% | 47.21% | 46.84% | NA |
| Indica I | 595 | 3.00% | 0.00% | 6.55% | 90.42% | NA |
| Indica II | 465 | 4.30% | 0.20% | 10.32% | 85.16% | NA |
| Indica III | 913 | 5.50% | 8.20% | 17.63% | 68.67% | NA |
| Indica Intermediate | 786 | 8.30% | 0.30% | 12.47% | 79.01% | NA |
| Temperate Japonica | 767 | 99.10% | 0.00% | 0.00% | 0.91% | NA |
| Tropical Japonica | 504 | 97.40% | 0.00% | 0.20% | 2.38% | NA |
| Japonica Intermediate | 241 | 97.50% | 0.00% | 0.41% | 2.07% | NA |
| VI/Aromatic | 96 | 92.70% | 0.00% | 2.08% | 5.21% | NA |
| Intermediate | 90 | 66.70% | 0.00% | 4.44% | 28.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0136521761 | C -> T | LOC_Os01g63040.1 | synonymous_variant ; p.Gln42Gln; LOW | synonymous_codon | Average:4.802; most accessible tissue: Callus, score: 8.148 | N | N | N | N |
| vg0136521761 | C -> DEL | LOC_Os01g63040.1 | N | frameshift_variant | Average:4.802; most accessible tissue: Callus, score: 8.148 | N | N | N | N |