| Variant ID: vg1212666305 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 12666305 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 286. )
AAGAACAGGATGGATAACCGTAAAAGGAAAATGACTGTTTTCCAGGAGGCACAAGGTAGTAGCCAGAGGCAGCGTATCAAGCCACTCCAAATTGGTGAAT[C/T]
TTCTTCCGCTGGTCAAGGACAGTCGCAACTGTTGAACATCGGTGGTGAGATCAAATTAGAGACTAATGAAAGTAATGAAGTAAACATCGAGCAAGCTAAT
ATTAGCTTGCTCGATGTTTACTTCATTACTTTCATTAGTCTCTAATTTGATCTCACCACCGATGTTCAACAGTTGCGACTGTCCTTGACCAGCGGAAGAA[G/A]
ATTCACCAATTTGGAGTGGCTTGATACGCTGCCTCTGGCTACTACCTTGTGCCTCCTGGAAAACAGTCATTTTCCTTTTACGGTTATCCATCCTGTTCTT
| 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 | 81.70% | 0.10% | 1.44% | 16.76% | NA |
| All Indica | 2759 | 83.70% | 0.00% | 1.49% | 14.82% | NA |
| All Japonica | 1512 | 75.90% | 0.10% | 1.12% | 22.95% | NA |
| Aus | 269 | 95.50% | 0.00% | 0.74% | 3.72% | NA |
| Indica I | 595 | 70.90% | 0.00% | 2.69% | 26.39% | NA |
| Indica II | 465 | 83.70% | 0.00% | 1.08% | 15.27% | NA |
| Indica III | 913 | 91.70% | 0.00% | 0.55% | 7.78% | NA |
| Indica Intermediate | 786 | 84.10% | 0.00% | 1.91% | 13.99% | NA |
| Temperate Japonica | 767 | 84.70% | 0.00% | 0.26% | 14.99% | NA |
| Tropical Japonica | 504 | 69.00% | 0.20% | 2.18% | 28.57% | NA |
| Japonica Intermediate | 241 | 61.80% | 0.00% | 1.66% | 36.51% | NA |
| VI/Aromatic | 96 | 83.30% | 2.10% | 4.17% | 10.42% | NA |
| Intermediate | 90 | 77.80% | 0.00% | 4.44% | 17.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1212666305 | C -> DEL | LOC_Os12g22430.1 | N | frameshift_variant | Average:5.272; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |
| vg1212666305 | C -> T | LOC_Os12g22430.1 | missense_variant ; p.Ser257Phe; MODERATE | nonsynonymous_codon ; S257F | Average:5.272; most accessible tissue: Zhenshan97 panicle, score: 16.188 | unknown | unknown | DELETERIOUS | 0.02 |