| Variant ID: vg1212666409 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 12666409 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 92. )
TTCCGCTGGTCAAGGACAGTCGCAACTGTTGAACATCGGTGGTGAGATCAAATTAGAGACTAATGAAAGTAATGAAGTAAACATCGAGCAAGCTAATCAG[C/T]
CGGTGCCAGTTCAGCAGGATCAGTCTCAGGAGAATAACAGTAGTGGAAGGGAGCAGTAGGTATGTTTCAACTGTTACAAGCCAGGTCACTTTGCAAGAGA
TCTCTTGCAAAGTGACCTGGCTTGTAACAGTTGAAACATACCTACTGCTCCCTTCCACTACTGTTATTCTCCTGAGACTGATCCTGCTGAACTGGCACCG[G/A]
CTGATTAGCTTGCTCGATGTTTACTTCATTACTTTCATTAGTCTCTAATTTGATCTCACCACCGATGTTCAACAGTTGCGACTGTCCTTGACCAGCGGAA
| 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 | 16.50% | 5.00% | 13.12% | 65.34% | NA |
| All Indica | 2759 | 3.60% | 8.50% | 18.41% | 69.55% | NA |
| All Japonica | 1512 | 43.50% | 0.00% | 1.19% | 55.29% | NA |
| Aus | 269 | 0.70% | 0.70% | 27.88% | 70.63% | NA |
| Indica I | 595 | 1.70% | 5.20% | 8.74% | 84.37% | NA |
| Indica II | 465 | 3.00% | 7.70% | 23.01% | 66.24% | NA |
| Indica III | 913 | 3.40% | 12.00% | 22.45% | 62.10% | NA |
| Indica Intermediate | 786 | 5.50% | 7.30% | 18.32% | 68.96% | NA |
| Temperate Japonica | 767 | 77.10% | 0.00% | 0.91% | 22.03% | NA |
| Tropical Japonica | 504 | 2.40% | 0.00% | 1.59% | 96.03% | NA |
| Japonica Intermediate | 241 | 22.80% | 0.00% | 1.24% | 75.93% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 10.42% | 89.58% | NA |
| Intermediate | 90 | 24.40% | 2.20% | 10.00% | 63.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1212666409 | C -> DEL | LOC_Os12g22430.1 | N | frameshift_variant | Average:5.218; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |
| vg1212666409 | C -> T | LOC_Os12g22430.1 | missense_variant ; p.Pro292Ser; MODERATE | nonsynonymous_codon ; P292S | Average:5.218; most accessible tissue: Zhenshan97 panicle, score: 16.188 | unknown | unknown | TOLERATED | 0.15 |