| Variant ID: vg1120444834 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 20444834 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
AATTTAGTGGTCCGGAGCGAAGCTAGAAAGATGGGCCCTTTAATACAACTCTGATAATATAATGATGTTTCTAACAAATGTAATGCATAAAAAAAACATT[C/T]
TTAGCAAACAAGTTGTATATCTTCCTCTCCTGTGCTTCCTAAATCTAAGTTCCTATGGCCTATGGGCTCCTATATCCATAGCATACATATATGGGGTTGG
CCAACCCCATATATGTATGCTATGGATATAGGAGCCCATAGGCCATAGGAACTTAGATTTAGGAAGCACAGGAGAGGAAGATATACAACTTGTTTGCTAA[G/A]
AATGTTTTTTTTATGCATTACATTTGTTAGAAACATCATTATATTATCAGAGTTGTATTAAAGGGCCCATCTTTCTAGCTTCGCTCCGGACCACTAAATT
| 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 | 77.60% | 0.50% | 2.16% | 19.68% | NA |
| All Indica | 2759 | 69.60% | 0.40% | 1.85% | 28.09% | NA |
| All Japonica | 1512 | 95.00% | 0.10% | 1.85% | 3.11% | NA |
| Aus | 269 | 54.60% | 4.50% | 8.18% | 32.71% | NA |
| Indica I | 595 | 52.40% | 0.00% | 0.67% | 46.89% | NA |
| Indica II | 465 | 78.70% | 0.00% | 1.51% | 19.78% | NA |
| Indica III | 913 | 69.60% | 0.80% | 2.63% | 27.05% | NA |
| Indica Intermediate | 786 | 77.40% | 0.60% | 2.04% | 19.97% | NA |
| Temperate Japonica | 767 | 96.60% | 0.00% | 2.48% | 0.91% | NA |
| Tropical Japonica | 504 | 90.50% | 0.20% | 1.39% | 7.94% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.00% | 0.83% | 0.00% | NA |
| VI/Aromatic | 96 | 86.50% | 0.00% | 1.04% | 12.50% | NA |
| Intermediate | 90 | 91.10% | 0.00% | 0.00% | 8.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1120444834 | C -> T | LOC_Os11g34880.1 | 3_prime_UTR_variant ; 290.0bp to feature; MODIFIER | silent_mutation | Average:35.831; most accessible tissue: Minghui63 flower, score: 63.41 | N | N | N | N |
| vg1120444834 | C -> DEL | N | N | silent_mutation | Average:35.831; most accessible tissue: Minghui63 flower, score: 63.41 | N | N | N | N |