| Variant ID: vg1212666278 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 12666278 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GACAAAGCAATTCGCCTTGAAGACAAGAAGAACAGGATGGATAACCGTAAAAGGAAAATGACTGTTTTCCAGGAGGCACAAGGTAGTAGCCAGAGGCAGC[G/A]
TATCAAGCCACTCCAAATTGGTGAATCTTCTTCCGCTGGTCAAGGACAGTCGCAACTGTTGAACATCGGTGGTGAGATCAAATTAGAGACTAATGAAAGT
ACTTTCATTAGTCTCTAATTTGATCTCACCACCGATGTTCAACAGTTGCGACTGTCCTTGACCAGCGGAAGAAGATTCACCAATTTGGAGTGGCTTGATA[C/T]
GCTGCCTCTGGCTACTACCTTGTGCCTCCTGGAAAACAGTCATTTTCCTTTTACGGTTATCCATCCTGTTCTTCTTGTCTTCAAGGCGAATTGCTTTGTC
| 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 | 76.30% | 1.20% | 3.43% | 19.13% | NA |
| All Indica | 2759 | 79.40% | 1.40% | 3.01% | 16.17% | NA |
| All Japonica | 1512 | 66.70% | 1.00% | 4.76% | 27.58% | NA |
| Aus | 269 | 94.40% | 0.00% | 0.37% | 5.20% | NA |
| Indica I | 595 | 68.60% | 0.30% | 3.36% | 27.73% | NA |
| Indica II | 465 | 79.40% | 2.40% | 2.15% | 16.13% | NA |
| Indica III | 913 | 85.50% | 2.10% | 3.50% | 8.87% | NA |
| Indica Intermediate | 786 | 80.40% | 1.00% | 2.67% | 15.90% | NA |
| Temperate Japonica | 767 | 83.30% | 0.00% | 0.65% | 16.04% | NA |
| Tropical Japonica | 504 | 49.00% | 3.00% | 10.71% | 37.30% | NA |
| Japonica Intermediate | 241 | 50.60% | 0.00% | 5.39% | 43.98% | NA |
| VI/Aromatic | 96 | 87.50% | 0.00% | 2.08% | 10.42% | NA |
| Intermediate | 90 | 76.70% | 0.00% | 4.44% | 18.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1212666278 | G -> DEL | LOC_Os12g22430.1 | N | frameshift_variant | Average:4.447; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1212666278 | G -> A | LOC_Os12g22430.1 | missense_variant ; p.Arg248His; MODERATE | nonsynonymous_codon ; R248H | Average:4.447; most accessible tissue: Minghui63 panicle, score: 7.125 | unknown | unknown | TOLERATED | 0.07 |