| Variant ID: vg1212666216 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 12666216 |
| Reference Allele: G | Alternative Allele: C |
| Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
TAAAGGATGAACTGTCAGTTACGTTAATCTCCCATGACTATGTTGATTTTCAGCAGCTGGTTGACAAAGCAATTCGCCTTGAAGACAAGAAGAACAGGAT[G/C]
GATAACCGTAAAAGGAAAATGACTGTTTTCCAGGAGGCACAAGGTAGTAGCCAGAGGCAGCGTATCAAGCCACTCCAAATTGGTGAATCTTCTTCCGCTG
CAGCGGAAGAAGATTCACCAATTTGGAGTGGCTTGATACGCTGCCTCTGGCTACTACCTTGTGCCTCCTGGAAAACAGTCATTTTCCTTTTACGGTTATC[C/G]
ATCCTGTTCTTCTTGTCTTCAAGGCGAATTGCTTTGTCAACCAGCTGCTGAAAATCAACATAGTCATGGGAGATTAACGTAACTGACAGTTCATCCTTTA
| Populations | Population Size | Frequency of G(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 18.90% | 0.10% | 25.98% | 55.04% | NA |
| All Indica | 2759 | 4.80% | 0.20% | 36.10% | 58.90% | NA |
| All Japonica | 1512 | 43.80% | 0.00% | 3.17% | 52.98% | NA |
| Aus | 269 | 23.40% | 0.00% | 45.72% | 30.86% | NA |
| Indica I | 595 | 1.50% | 0.00% | 17.98% | 80.50% | NA |
| Indica II | 465 | 3.70% | 0.00% | 30.11% | 66.24% | NA |
| Indica III | 913 | 4.90% | 0.40% | 53.01% | 41.62% | NA |
| Indica Intermediate | 786 | 7.90% | 0.10% | 33.72% | 58.27% | NA |
| Temperate Japonica | 767 | 77.60% | 0.00% | 1.17% | 21.25% | NA |
| Tropical Japonica | 504 | 2.40% | 0.00% | 5.36% | 92.26% | NA |
| Japonica Intermediate | 241 | 23.20% | 0.00% | 4.98% | 71.78% | NA |
| VI/Aromatic | 96 | 5.20% | 0.00% | 45.83% | 48.96% | NA |
| Intermediate | 90 | 31.10% | 0.00% | 18.89% | 50.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1212666216 | G -> C | LOC_Os12g22430.1 | missense_variant ; p.Met227Ile; MODERATE | nonsynonymous_codon ; M227I | Average:4.447; most accessible tissue: Minghui63 panicle, score: 7.125 | unknown | unknown | DELETERIOUS | 0.04 |
| vg1212666216 | G -> DEL | LOC_Os12g22430.1 | N | frameshift_variant | Average:4.447; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |