| Variant ID: vg1212666282 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 12666282 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 268. )
AAGCAATTCGCCTTGAAGACAAGAAGAACAGGATGGATAACCGTAAAAGGAAAATGACTGTTTTCCAGGAGGCACAAGGTAGTAGCCAGAGGCAGCGTAT[C/T]
AAGCCACTCCAAATTGGTGAATCTTCTTCCGCTGGTCAAGGACAGTCGCAACTGTTGAACATCGGTGGTGAGATCAAATTAGAGACTAATGAAAGTAATG
CATTACTTTCATTAGTCTCTAATTTGATCTCACCACCGATGTTCAACAGTTGCGACTGTCCTTGACCAGCGGAAGAAGATTCACCAATTTGGAGTGGCTT[G/A]
ATACGCTGCCTCTGGCTACTACCTTGTGCCTCCTGGAAAACAGTCATTTTCCTTTTACGGTTATCCATCCTGTTCTTCTTGTCTTCAAGGCGAATTGCTT
| 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 | 79.80% | 0.00% | 1.99% | 18.18% | NA |
| All Indica | 2759 | 83.30% | 0.00% | 1.67% | 15.01% | NA |
| All Japonica | 1512 | 70.50% | 0.00% | 2.71% | 26.79% | NA |
| Aus | 269 | 94.80% | 0.00% | 0.00% | 5.20% | NA |
| Indica I | 595 | 70.80% | 0.00% | 2.69% | 26.55% | NA |
| Indica II | 465 | 83.40% | 0.00% | 1.29% | 15.27% | NA |
| Indica III | 913 | 91.30% | 0.10% | 0.77% | 7.78% | NA |
| Indica Intermediate | 786 | 83.30% | 0.00% | 2.16% | 14.50% | NA |
| Temperate Japonica | 767 | 83.40% | 0.00% | 0.65% | 15.91% | NA |
| Tropical Japonica | 504 | 59.70% | 0.00% | 4.76% | 35.52% | NA |
| Japonica Intermediate | 241 | 51.90% | 0.00% | 4.98% | 43.15% | NA |
| VI/Aromatic | 96 | 87.50% | 0.00% | 2.08% | 10.42% | NA |
| Intermediate | 90 | 76.70% | 0.00% | 5.56% | 17.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1212666282 | C -> DEL | LOC_Os12g22430.1 | N | frameshift_variant | Average:4.447; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1212666282 | C -> T | LOC_Os12g22430.1 | synonymous_variant ; p.Ile249Ile; LOW | synonymous_codon | Average:4.447; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |