| Variant ID: vg1225600884 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 25600884 |
| 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, others allele: 0.00, population size: 313. )
GCAACAAGCCGAGCCTTGTACTTTTCAATAGTACCGTCAGGCCTAAGCTTCTTCTTGAACACCCACTTGCACCCCACAGGTTTACACCCATAGGGTCGCT[C/T]
TGTCACCTCCCAAGTCCCGTTAGCGATAATGGAATCCATTTCACTACGGACAGCCTCCTTCCAGTAGTCTGCATCAGGAGATGCATATGCTTCTGAAATT
AATTTCAGAAGCATATGCATCTCCTGATGCAGACTACTGGAAGGAGGCTGTCCGTAGTGAAATGGATTCCATTATCGCTAACGGGACTTGGGAGGTGACA[G/A]
AGCGACCCTATGGGTGTAAACCTGTGGGGTGCAAGTGGGTGTTCAAGAAGAAGCTTAGGCCTGACGGTACTATTGAAAAGTACAAGGCTCGGCTTGTTGC
| 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 | 53.10% | 0.30% | 4.87% | 41.77% | NA |
| All Indica | 2759 | 39.70% | 0.10% | 0.43% | 59.73% | NA |
| All Japonica | 1512 | 86.00% | 0.40% | 13.56% | 0.07% | NA |
| Aus | 269 | 0.40% | 0.00% | 0.37% | 99.26% | NA |
| Indica I | 595 | 85.90% | 0.00% | 0.50% | 13.61% | NA |
| Indica II | 465 | 14.00% | 0.00% | 0.65% | 85.38% | NA |
| Indica III | 913 | 26.10% | 0.00% | 0.11% | 73.82% | NA |
| Indica Intermediate | 786 | 35.90% | 0.40% | 0.64% | 63.10% | NA |
| Temperate Japonica | 767 | 85.30% | 0.50% | 14.21% | 0.00% | NA |
| Tropical Japonica | 504 | 96.00% | 0.00% | 3.97% | 0.00% | NA |
| Japonica Intermediate | 241 | 67.20% | 0.80% | 31.54% | 0.41% | NA |
| VI/Aromatic | 96 | 58.30% | 5.20% | 9.38% | 27.08% | NA |
| Intermediate | 90 | 61.10% | 0.00% | 3.33% | 35.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1225600884 | C -> DEL | LOC_Os12g41280.1 | N | frameshift_variant | Average:8.674; most accessible tissue: Zhenshan97 root, score: 20.427 | N | N | N | N |
| vg1225600884 | C -> T | LOC_Os12g41280.1 | missense_variant ; p.Glu827Lys; MODERATE | nonsynonymous_codon ; E827K | Average:8.674; most accessible tissue: Zhenshan97 root, score: 20.427 | unknown | unknown | DELETERIOUS | 0.03 |