| Variant ID: vg1221990395 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 21990395 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TTACTAATAAATAATCTCTCACAACATGAAGGTGACGTCGGGCATGGCCATCCCAACAGACCCTTCAGGTACTTACCACTGCAGGCCGATTCCAGCAGGA[T/A]
ACTCGAAGGTCGAAGTTGAGTTGGTCGAAGGCGCGTACGAGGACCTCGAGCTGGATTACCCTGGAGGAGACGGTGAGACGCATCTACGAGACACATGACA
TGTCATGTGTCTCGTAGATGCGTCTCACCGTCTCCTCCAGGGTAATCCAGCTCGAGGTCCTCGTACGCGCCTTCGACCAACTCAACTTCGACCTTCGAGT[A/T]
TCCTGCTGGAATCGGCCTGCAGTGGTAAGTACCTGAAGGGTCTGTTGGGATGGCCATGCCCGACGTCACCTTCATGTTGTGAGAGATTATTTATTAGTAA
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 72.00% | 0.20% | 11.11% | 16.69% | NA |
| All Indica | 2759 | 64.70% | 0.00% | 15.51% | 19.75% | NA |
| All Japonica | 1512 | 88.20% | 0.60% | 2.78% | 8.40% | NA |
| Aus | 269 | 46.50% | 0.00% | 13.38% | 40.15% | NA |
| Indica I | 595 | 69.40% | 0.00% | 7.06% | 23.53% | NA |
| Indica II | 465 | 74.60% | 0.00% | 13.12% | 12.26% | NA |
| Indica III | 913 | 57.40% | 0.00% | 21.69% | 20.92% | NA |
| Indica Intermediate | 786 | 63.90% | 0.00% | 16.16% | 19.97% | NA |
| Temperate Japonica | 767 | 91.30% | 1.20% | 4.43% | 3.13% | NA |
| Tropical Japonica | 504 | 79.80% | 0.00% | 0.79% | 19.44% | NA |
| Japonica Intermediate | 241 | 96.30% | 0.00% | 1.66% | 2.07% | NA |
| VI/Aromatic | 96 | 85.40% | 0.00% | 13.54% | 1.04% | NA |
| Intermediate | 90 | 84.40% | 0.00% | 6.67% | 8.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1221990395 | T -> DEL | LOC_Os12g35970.1 | N | frameshift_variant | Average:19.621; most accessible tissue: Minghui63 young leaf, score: 51.901 | N | N | N | N |
| vg1221990395 | T -> A | LOC_Os12g35970.1 | missense_variant ; p.Tyr151Asn; MODERATE | nonsynonymous_codon ; Y151N | Average:19.621; most accessible tissue: Minghui63 young leaf, score: 51.901 | unknown | unknown | DELETERIOUS | 0.00 |