| Variant ID: vg1209004310 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 9004310 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
AATGGTGACTTAGCTTTTTAGTGTTCCCCCGGTAATAGCAGATGTAGCCGATGTGTGGAGAAAGTCGTCCATCAATCCCAATAAAAACACCAGTCGGCGG[C/T]
GATGGCAGCCGCCGGAAGTGAAGACATGGTCGCCATCAACAACGGCAGCGGATTACACCAACCGTGGAGGCGAAGAAACCGGTCGGCAGTGATGACGGCG
CGCCGTCATCACTGCCGACCGGTTTCTTCGCCTCCACGGTTGGTGTAATCCGCTGCCGTTGTTGATGGCGACCATGTCTTCACTTCCGGCGGCTGCCATC[G/A]
CCGCCGACTGGTGTTTTTATTGGGATTGATGGACGACTTTCTCCACACATCGGCTACATCTGCTATTACCGGGGGAACACTAAAAAGCTAAGTCACCATT
| 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 | 78.60% | 0.20% | 0.85% | 20.33% | NA |
| All Indica | 2759 | 66.10% | 0.00% | 1.23% | 32.69% | NA |
| All Japonica | 1512 | 99.00% | 0.00% | 0.00% | 0.99% | NA |
| Aus | 269 | 81.80% | 4.10% | 2.23% | 11.90% | NA |
| Indica I | 595 | 59.00% | 0.00% | 1.51% | 39.50% | NA |
| Indica II | 465 | 66.70% | 0.00% | 0.65% | 32.69% | NA |
| Indica III | 913 | 68.60% | 0.00% | 1.20% | 30.23% | NA |
| Indica Intermediate | 786 | 68.20% | 0.00% | 1.40% | 30.41% | NA |
| Temperate Japonica | 767 | 99.00% | 0.00% | 0.00% | 1.04% | NA |
| Tropical Japonica | 504 | 99.40% | 0.00% | 0.00% | 0.60% | NA |
| Japonica Intermediate | 241 | 98.30% | 0.00% | 0.00% | 1.66% | NA |
| VI/Aromatic | 96 | 95.80% | 0.00% | 0.00% | 4.17% | NA |
| Intermediate | 90 | 91.10% | 0.00% | 0.00% | 8.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1209004310 | C -> DEL | LOC_Os12g15770.1 | N | frameshift_variant | Average:40.672; most accessible tissue: Callus, score: 70.638 | N | N | N | N |
| vg1209004310 | C -> T | LOC_Os12g15770.1 | missense_variant ; p.Ala110Thr; MODERATE | nonsynonymous_codon ; A110T | Average:40.672; most accessible tissue: Callus, score: 70.638 | unknown | unknown | DELETERIOUS | 0.04 |