| Variant ID: vg1105183725 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 5183725 |
| Reference Allele: G | Alternative Allele: C |
| Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
AATGCTTCATGGCACCTTATATTGGTATCTTAAAGGTGACCAATACTATTATGCTCCTAAATGTGCAACTACTGCTGATGCTCACGCGATTACATTGATT[G/C]
GATCTGGGTTGGCTTCTAAGAACAATATGCCTGAGACGTTCTATTCAGCCAGAGATTCACATGGGACTAAATCCCATCCTGACCATAAGATGCGTGACTT
AAGTCACGCATCTTATGGTCAGGATGGGATTTAGTCCCATGTGAATCTCTGGCTGAATAGAACGTCTCAGGCATATTGTTCTTAGAAGCCAACCCAGATC[C/G]
AATCAATGTAATCGCGTGAGCATCAGCAGTAGTTGCACATTTAGGAGCATAATAGTATTGGTCACCTTTAAGATACCAATATAAGGTGCCATGAAGCATT
| Populations | Population Size | Frequency of G(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 66.80% | 1.60% | 0.78% | 30.81% | NA |
| All Indica | 2759 | 48.30% | 2.50% | 1.09% | 48.10% | NA |
| All Japonica | 1512 | 98.70% | 0.10% | 0.07% | 1.12% | NA |
| Aus | 269 | 67.30% | 1.50% | 2.23% | 29.00% | NA |
| Indica I | 595 | 26.40% | 1.70% | 2.18% | 69.75% | NA |
| Indica II | 465 | 21.90% | 0.40% | 1.08% | 76.56% | NA |
| Indica III | 913 | 68.30% | 5.30% | 0.33% | 26.07% | NA |
| Indica Intermediate | 786 | 57.10% | 1.30% | 1.15% | 40.46% | NA |
| Temperate Japonica | 767 | 97.90% | 0.00% | 0.13% | 1.96% | NA |
| Tropical Japonica | 504 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.00% | 0.00% | 0.83% | NA |
| VI/Aromatic | 96 | 91.70% | 0.00% | 0.00% | 8.33% | NA |
| Intermediate | 90 | 68.90% | 2.20% | 0.00% | 28.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1105183725 | G -> DEL | LOC_Os11g09710.1 | N | frameshift_variant | Average:17.63; most accessible tissue: Callus, score: 89.679 | N | N | N | N |
| vg1105183725 | G -> C | LOC_Os11g09710.1 | missense_variant ; p.Gly267Arg; MODERATE | nonsynonymous_codon ; G267R | Average:17.63; most accessible tissue: Callus, score: 89.679 | unknown | unknown | TOLERATED | 0.32 |