| Variant ID: vg1101255731 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 1255731 |
| Reference Allele: A | Alternative Allele: C |
| Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
TACGCATCTATCTTCCTATGAAATGTTCTCTCTTGTTTTCAATAAAACTATGCTTGCACTGAATCATTTGTTTTTATAATTTTGCAGGACAAGTTTGAAA[A/C]
TGAAGATCCAGATATTAAAATTGATGTATACAAAGATGAGATAATGGAACATGCCAAGTCTCTTTGGATTAACTGGCGTGGAGATTTGCATCGACATTTT
AAAATGTCGATGCAAATCTCCACGCCAGTTAATCCAAAGAGACTTGGCATGTTCCATTATCTCATCTTTGTATACATCAATTTTAATATCTGGATCTTCA[T/G]
TTTCAAACTTGTCCTGCAAAATTATAAAAACAAATGATTCAGTGCAAGCATAGTTTTATTGAAAACAAGAGAGAACATTTCATAGGAAGATAGATGCGTA
| 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 | 68.50% | 0.10% | 7.47% | 23.85% | NA |
| All Indica | 2759 | 52.20% | 0.20% | 11.82% | 35.74% | NA |
| All Japonica | 1512 | 98.10% | 0.00% | 0.13% | 1.79% | NA |
| Aus | 269 | 71.00% | 0.40% | 5.58% | 23.05% | NA |
| Indica I | 595 | 24.50% | 0.00% | 21.85% | 53.61% | NA |
| Indica II | 465 | 49.20% | 0.20% | 12.26% | 38.28% | NA |
| Indica III | 913 | 71.10% | 0.10% | 5.37% | 23.44% | NA |
| Indica Intermediate | 786 | 53.10% | 0.50% | 11.45% | 34.99% | NA |
| Temperate Japonica | 767 | 98.60% | 0.00% | 0.00% | 1.43% | NA |
| Tropical Japonica | 504 | 98.20% | 0.00% | 0.40% | 1.39% | NA |
| Japonica Intermediate | 241 | 96.30% | 0.00% | 0.00% | 3.73% | NA |
| VI/Aromatic | 96 | 64.60% | 0.00% | 4.17% | 31.25% | NA |
| Intermediate | 90 | 68.90% | 0.00% | 6.67% | 24.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1101255731 | A -> DEL | LOC_Os11g03340.1 | N | frameshift_variant | Average:6.762; most accessible tissue: Callus, score: 12.962 | N | N | N | N |
| vg1101255731 | A -> C | LOC_Os11g03340.1 | missense_variant ; p.Asn191Thr; MODERATE | nonsynonymous_codon | Average:6.762; most accessible tissue: Callus, score: 12.962 | unknown | unknown | DELETERIOUS | 0.01 |