| Variant ID: vg1222420133 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 22420133 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
GCACACGAACTAAACACAGCCTAAATAAAGTGCTCAAGAATATACATGAGATTATATTCACAACATTGCCCATTCAGGTAGCCATCGAAGAAGAGGTAGC[G/A]
GATACGTTGGTAGCCGATTCTTGTTCTTTCTTCTTCACCACCAGACGCTCCCGTGCTTCCTTCACCAGCGAAGCATAATTCCCGACAGGTTTCCCTTGCT
AGCAAGGGAAACCTGTCGGGAATTATGCTTCGCTGGTGAAGGAAGCACGGGAGCGTCTGGTGGTGAAGAAGAAAGAACAAGAATCGGCTACCAACGTATC[C/T]
GCTACCTCTTCTTCGATGGCTACCTGAATGGGCAATGTTGTGAATATAATCTCATGTATATTCTTGAGCACTTTATTTAGGCTGTGTTTAGTTCGTGTGC
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 50.90% | 1.20% | 4.23% | 43.72% | NA |
| All Indica | 2759 | 38.20% | 0.10% | 0.98% | 60.64% | NA |
| All Japonica | 1512 | 72.50% | 3.20% | 11.04% | 13.23% | NA |
| Aus | 269 | 36.10% | 0.00% | 0.74% | 63.20% | NA |
| Indica I | 595 | 39.80% | 0.00% | 1.85% | 58.32% | NA |
| Indica II | 465 | 20.60% | 0.20% | 1.29% | 77.85% | NA |
| Indica III | 913 | 44.70% | 0.00% | 0.33% | 54.98% | NA |
| Indica Intermediate | 786 | 39.90% | 0.40% | 0.89% | 58.78% | NA |
| Temperate Japonica | 767 | 67.00% | 6.30% | 18.25% | 8.47% | NA |
| Tropical Japonica | 504 | 74.60% | 0.20% | 3.37% | 21.83% | NA |
| Japonica Intermediate | 241 | 85.50% | 0.00% | 4.15% | 10.37% | NA |
| VI/Aromatic | 96 | 94.80% | 0.00% | 0.00% | 5.21% | NA |
| Intermediate | 90 | 72.20% | 3.30% | 4.44% | 20.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1222420133 | G -> DEL | N | N | silent_mutation | Average:10.856; most accessible tissue: Callus, score: 57.458 | N | N | N | N |
| vg1222420133 | G -> A | LOC_Os12g36620.1 | splice_region_variant&intron_variant ; LOW | silent_mutation | Average:10.856; most accessible tissue: Callus, score: 57.458 | N | N | N | N |
| vg1222420133 | G -> A | LOC_Os12g36600.1 | downstream_gene_variant ; 4517.0bp to feature; MODIFIER | silent_mutation | Average:10.856; most accessible tissue: Callus, score: 57.458 | N | N | N | N |
| vg1222420133 | G -> A | LOC_Os12g36610.1 | downstream_gene_variant ; 868.0bp to feature; MODIFIER | silent_mutation | Average:10.856; most accessible tissue: Callus, score: 57.458 | N | N | N | N |