| Variant ID: vg1221990382 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 21990382 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TTATATATGTTGATTACTAATAAATAATCTCTCACAACATGAAGGTGACGTCGGGCATGGCCATCCCAACAGACCCTTCAGGTACTTACCACTGCAGGCC[G/A]
ATTCCAGCAGGATACTCGAAGGTCGAAGTTGAGTTGGTCGAAGGCGCGTACGAGGACCTCGAGCTGGATTACCCTGGAGGAGACGGTGAGACGCATCTAC
GTAGATGCGTCTCACCGTCTCCTCCAGGGTAATCCAGCTCGAGGTCCTCGTACGCGCCTTCGACCAACTCAACTTCGACCTTCGAGTATCCTGCTGGAAT[C/T]
GGCCTGCAGTGGTAAGTACCTGAAGGGTCTGTTGGGATGGCCATGCCCGACGTCACCTTCATGTTGTGAGAGATTATTTATTAGTAATCAACATATATAA
| 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 | 65.90% | 1.20% | 10.35% | 22.60% | NA |
| All Indica | 2759 | 52.70% | 2.00% | 10.95% | 34.36% | NA |
| All Japonica | 1512 | 91.30% | 0.00% | 6.88% | 1.79% | NA |
| Aus | 269 | 46.50% | 0.00% | 22.30% | 31.23% | NA |
| Indica I | 595 | 67.90% | 0.50% | 1.68% | 29.92% | NA |
| Indica II | 465 | 69.70% | 0.20% | 3.23% | 26.88% | NA |
| Indica III | 913 | 31.40% | 5.10% | 19.17% | 44.25% | NA |
| Indica Intermediate | 786 | 56.00% | 0.40% | 12.98% | 30.66% | NA |
| Temperate Japonica | 767 | 96.70% | 0.00% | 2.74% | 0.52% | NA |
| Tropical Japonica | 504 | 80.00% | 0.00% | 15.67% | 4.37% | NA |
| Japonica Intermediate | 241 | 97.90% | 0.00% | 1.66% | 0.41% | NA |
| VI/Aromatic | 96 | 81.20% | 1.00% | 16.67% | 1.04% | NA |
| Intermediate | 90 | 82.20% | 1.10% | 7.78% | 8.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1221990382 | G -> DEL | LOC_Os12g35970.1 | N | frameshift_variant | Average:19.176; most accessible tissue: Minghui63 young leaf, score: 51.901 | N | N | N | N |
| vg1221990382 | G -> A | LOC_Os12g35970.1 | synonymous_variant ; p.Pro146Pro; LOW | synonymous_codon | Average:19.176; most accessible tissue: Minghui63 young leaf, score: 51.901 | N | N | N | N |