| Variant ID: vg1221990390 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 21990390 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GTTGATTACTAATAAATAATCTCTCACAACATGAAGGTGACGTCGGGCATGGCCATCCCAACAGACCCTTCAGGTACTTACCACTGCAGGCCGATTCCAG[C/T]
AGGATACTCGAAGGTCGAAGTTGAGTTGGTCGAAGGCGCGTACGAGGACCTCGAGCTGGATTACCCTGGAGGAGACGGTGAGACGCATCTACGAGACACA
TGTGTCTCGTAGATGCGTCTCACCGTCTCCTCCAGGGTAATCCAGCTCGAGGTCCTCGTACGCGCCTTCGACCAACTCAACTTCGACCTTCGAGTATCCT[G/A]
CTGGAATCGGCCTGCAGTGGTAAGTACCTGAAGGGTCTGTTGGGATGGCCATGCCCGACGTCACCTTCATGTTGTGAGAGATTATTTATTAGTAATCAAC
| 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 | 65.90% | 1.20% | 10.07% | 22.81% | NA |
| All Indica | 2759 | 52.80% | 2.00% | 11.63% | 33.56% | NA |
| All Japonica | 1512 | 91.30% | 0.00% | 5.89% | 2.78% | NA |
| Aus | 269 | 46.50% | 0.00% | 16.36% | 37.17% | NA |
| Indica I | 595 | 67.70% | 0.50% | 1.85% | 29.92% | NA |
| Indica II | 465 | 69.50% | 0.20% | 3.23% | 27.10% | NA |
| Indica III | 913 | 32.10% | 5.10% | 21.25% | 41.51% | NA |
| Indica Intermediate | 786 | 55.90% | 0.40% | 12.85% | 30.92% | NA |
| Temperate Japonica | 767 | 96.70% | 0.00% | 2.22% | 1.04% | NA |
| Tropical Japonica | 504 | 80.00% | 0.00% | 13.69% | 6.35% | NA |
| Japonica Intermediate | 241 | 97.90% | 0.00% | 1.24% | 0.83% | NA |
| VI/Aromatic | 96 | 81.20% | 1.00% | 16.67% | 1.04% | NA |
| Intermediate | 90 | 82.20% | 1.10% | 6.67% | 10.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1221990390 | C -> DEL | LOC_Os12g35970.1 | N | frameshift_variant | Average:19.247; most accessible tissue: Minghui63 young leaf, score: 51.901 | N | N | N | N |
| vg1221990390 | C -> T | LOC_Os12g35970.1 | missense_variant ; p.Ala149Val; MODERATE | nonsynonymous_codon ; A149V | Average:19.247; most accessible tissue: Minghui63 young leaf, score: 51.901 | unknown | unknown | DELETERIOUS | 0.01 |