| Variant ID: vg1123252881 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 23252881 |
| 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: 259. )
CTAACTAATGACTAGTTGAATCATCTGTTCATCACAAGATCGATCAGTATCTGCATGTCCACACACATCTCAATATCTCATGGCTACTCGAATTCGAAGG[C/T]
GCTCCAGTCGATCTTGGCCCATTCTTCGTTGATCAGAGCCTCGAGCTTGGCCTGATCGGCGAGGTAGCTCTCGCCGACGACGTAGCAGCCGTTGTCCTCG
CGAGGACAACGGCTGCTACGTCGTCGGCGAGAGCTACCTCGCCGATCAGGCCAAGCTCGAGGCTCTGATCAACGAAGAATGGGCCAAGATCGACTGGAGC[G/A]
CCTTCGAATTCGAGTAGCCATGAGATATTGAGATGTGTGTGGACATGCAGATACTGATCGATCTTGTGATGAACAGATGATTCAACTAGTCATTAGTTAG
| 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 | 95.90% | 4.10% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 93.80% | 6.20% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Aus | 269 | 91.80% | 8.20% | 0.00% | 0.00% | NA |
| Indica I | 595 | 85.00% | 15.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 98.70% | 1.30% | 0.00% | 0.00% | NA |
| Indica III | 913 | 96.10% | 3.90% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 95.00% | 5.00% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 97.80% | 2.20% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1123252881 | C -> T | LOC_Os11g39060.1 | missense_variant ; p.Ala131Thr; MODERATE | nonsynonymous_codon ; A131T | Average:65.848; most accessible tissue: Minghui63 root, score: 81.505 | unknown | unknown | TOLERATED | 0.26 |