| Variant ID: vg1105183356 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 5183356 |
| Reference Allele: A | Alternative Allele: C |
| Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, C: 0.01, others allele: 0.00, population size: 213. )
ATATTCAGTTGCTGCCACAATTGACGCCACTCGTAGGGTAGAAGGGGCCAAGAAAGGATTGATAATCTCCACTCCACTTGACGTACCAGAGATGGCTAAA[A/C]
CATATGAGCAAGTCACTGGTTTTGAGCTTGGGAAAGAACCCCCGGAGGAGTTGTTTGAGACGTACGACAACTGCTCTCTCATTATGGAAGTTGTTAAAGC
GCTTTAACAACTTCCATAATGAGAGAGCAGTTGTCGTACGTCTCAAACAACTCCTCCGGGGGTTCTTTCCCAAGCTCAAAACCAGTGACTTGCTCATATG[T/G]
TTTAGCCATCTCTGGTACGTCAAGTGGAGTGGAGATTATCAATCCTTTCTTGGCCCCTTCTACCCTACGAGTGGCGTCAATTGTGGCAGCAACTGAATAT
| Populations | Population Size | Frequency of A(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 48.80% | 19.30% | 0.91% | 31.04% | NA |
| All Indica | 2759 | 22.30% | 28.10% | 1.30% | 48.24% | NA |
| All Japonica | 1512 | 91.80% | 6.90% | 0.07% | 1.26% | NA |
| Aus | 269 | 60.20% | 7.10% | 1.49% | 31.23% | NA |
| Indica I | 595 | 26.40% | 2.00% | 2.02% | 69.58% | NA |
| Indica II | 465 | 7.70% | 12.90% | 2.15% | 77.20% | NA |
| Indica III | 913 | 18.80% | 54.20% | 0.88% | 26.07% | NA |
| Indica Intermediate | 786 | 31.90% | 26.60% | 0.76% | 40.71% | NA |
| Temperate Japonica | 767 | 97.00% | 0.70% | 0.13% | 2.22% | NA |
| Tropical Japonica | 504 | 83.50% | 16.50% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 92.50% | 6.60% | 0.00% | 0.83% | NA |
| VI/Aromatic | 96 | 91.70% | 0.00% | 0.00% | 8.33% | NA |
| Intermediate | 90 | 57.80% | 12.20% | 2.22% | 27.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1105183356 | A -> DEL | LOC_Os11g09710.1 | N | frameshift_variant | Average:15.54; most accessible tissue: Callus, score: 72.073 | N | N | N | N |
| vg1105183356 | A -> C | LOC_Os11g09710.1 | missense_variant ; p.Thr144Pro; MODERATE | nonsynonymous_codon ; T144P | Average:15.54; most accessible tissue: Callus, score: 72.073 | unknown | unknown | DELETERIOUS | 0.03 |