| Variant ID: vg0143001958 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 43001958 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CCGCGGCCAGAAGCTCTCGCTTCATGGCCTTGAAGCTCCGGCGAGAAACGTGAGCACACGCTCCCCCATCGACGGTGGCAATGGTGGCCCCAGGCTCTTG[G/A]
AAACCTAGGTCATCATCGCCGTCATCGATGTCCTCGGCGGGGGCCTTCTGCTTGGCCTCACTTCGCCGATTGCCGGAAGGAACCGCCGGGGACTTGCCCT
AGGGCAAGTCCCCGGCGGTTCCTTCCGGCAATCGGCGAAGTGAGGCCAAGCAGAAGGCCCCCGCCGAGGACATCGATGACGGCGATGATGACCTAGGTTT[C/T]
CAAGAGCCTGGGGCCACCATTGCCACCGTCGATGGGGGAGCGTGTGCTCACGTTTCTCGCCGGAGCTTCAAGGCCATGAAGCGAGAGCTTCTGGCCGCGG
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 12.20% | 0.30% | 13.06% | 74.48% | NA |
| All Indica | 2759 | 4.70% | 0.40% | 14.68% | 80.21% | NA |
| All Japonica | 1512 | 27.70% | 0.00% | 4.83% | 67.46% | NA |
| Aus | 269 | 1.10% | 0.00% | 36.80% | 62.08% | NA |
| Indica I | 595 | 4.50% | 0.00% | 7.39% | 88.07% | NA |
| Indica II | 465 | 3.40% | 0.20% | 8.82% | 87.53% | NA |
| Indica III | 913 | 5.30% | 1.00% | 22.34% | 71.41% | NA |
| Indica Intermediate | 786 | 4.80% | 0.30% | 14.76% | 80.15% | NA |
| Temperate Japonica | 767 | 39.00% | 0.00% | 3.00% | 58.02% | NA |
| Tropical Japonica | 504 | 19.80% | 0.00% | 7.74% | 72.42% | NA |
| Japonica Intermediate | 241 | 8.30% | 0.00% | 4.56% | 87.14% | NA |
| VI/Aromatic | 96 | 9.40% | 0.00% | 27.08% | 63.54% | NA |
| Intermediate | 90 | 18.90% | 0.00% | 15.56% | 65.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0143001958 | G -> A | LOC_Os01g74230.1 | synonymous_variant ; p.Phe372Phe; LOW | synonymous_codon | Average:5.972; most accessible tissue: Callus, score: 12.637 | N | N | N | N |
| vg0143001958 | G -> DEL | LOC_Os01g74230.1 | N | frameshift_variant | Average:5.972; most accessible tissue: Callus, score: 12.637 | N | N | N | N |