| Variant ID: vg1212666312 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 12666312 |
| 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: 277. )
GGATGGATAACCGTAAAAGGAAAATGACTGTTTTCCAGGAGGCACAAGGTAGTAGCCAGAGGCAGCGTATCAAGCCACTCCAAATTGGTGAATCTTCTTC[C/T]
GCTGGTCAAGGACAGTCGCAACTGTTGAACATCGGTGGTGAGATCAAATTAGAGACTAATGAAAGTAATGAAGTAAACATCGAGCAAGCTAATCAGCCGG
CCGGCTGATTAGCTTGCTCGATGTTTACTTCATTACTTTCATTAGTCTCTAATTTGATCTCACCACCGATGTTCAACAGTTGCGACTGTCCTTGACCAGC[G/A]
GAAGAAGATTCACCAATTTGGAGTGGCTTGATACGCTGCCTCTGGCTACTACCTTGTGCCTCCTGGAAAACAGTCATTTTCCTTTTACGGTTATCCATCC
| 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 | 55.50% | 9.50% | 17.25% | 17.69% | NA |
| All Indica | 2759 | 51.80% | 10.20% | 21.89% | 16.06% | NA |
| All Japonica | 1512 | 54.40% | 10.30% | 12.04% | 23.28% | NA |
| Aus | 269 | 92.90% | 0.00% | 3.35% | 3.72% | NA |
| Indica I | 595 | 31.90% | 6.40% | 32.44% | 29.24% | NA |
| Indica II | 465 | 53.10% | 11.40% | 19.14% | 16.34% | NA |
| Indica III | 913 | 61.20% | 13.80% | 17.20% | 7.78% | NA |
| Indica Intermediate | 786 | 55.20% | 8.30% | 20.99% | 15.52% | NA |
| Temperate Japonica | 767 | 80.10% | 1.70% | 3.00% | 15.25% | NA |
| Tropical Japonica | 504 | 23.60% | 23.00% | 25.00% | 28.37% | NA |
| Japonica Intermediate | 241 | 37.30% | 10.80% | 13.69% | 38.17% | NA |
| VI/Aromatic | 96 | 75.00% | 5.20% | 9.38% | 10.42% | NA |
| Intermediate | 90 | 54.40% | 10.00% | 12.22% | 23.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1212666312 | C -> DEL | LOC_Os12g22430.1 | N | frameshift_variant | Average:5.272; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |
| vg1212666312 | C -> T | LOC_Os12g22430.1 | synonymous_variant ; p.Ser259Ser; LOW | synonymous_codon | Average:5.272; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |