| Variant ID: vg1101255638 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 1255638 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TTGTTCGTGATCGGAACATTACTCCGGTCAAAGTGAAGAAATGGTCAGACATTAGTAACACAGAGCAGGAACACATATTTGCCTCGATTACGGTACGCAT[C/T]
TATCTTCCTATGAAATGTTCTCTCTTGTTTTCAATAAAACTATGCTTGCACTGAATCATTTGTTTTTATAATTTTGCAGGACAAGTTTGAAAATGAAGAT
ATCTTCATTTTCAAACTTGTCCTGCAAAATTATAAAAACAAATGATTCAGTGCAAGCATAGTTTTATTGAAAACAAGAGAGAACATTTCATAGGAAGATA[G/A]
ATGCGTACCGTAATCGAGGCAAATATGTGTTCCTGCTCTGTGTTACTAATGTCTGACCATTTCTTCACTTTGACCGGAGTAATGTTCCGATCACGAACAA
| 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 | 44.10% | 0.30% | 4.30% | 51.40% | NA |
| All Indica | 2759 | 12.30% | 0.30% | 5.36% | 82.02% | NA |
| All Japonica | 1512 | 97.60% | 0.00% | 0.33% | 2.12% | NA |
| Aus | 269 | 68.00% | 0.70% | 7.06% | 24.16% | NA |
| Indica I | 595 | 12.90% | 0.00% | 6.72% | 80.34% | NA |
| Indica II | 465 | 7.10% | 0.60% | 3.66% | 88.60% | NA |
| Indica III | 913 | 8.40% | 0.30% | 4.38% | 86.86% | NA |
| Indica Intermediate | 786 | 19.30% | 0.40% | 6.49% | 73.79% | NA |
| Temperate Japonica | 767 | 97.80% | 0.00% | 0.65% | 1.56% | NA |
| Tropical Japonica | 504 | 97.80% | 0.00% | 0.00% | 2.18% | NA |
| Japonica Intermediate | 241 | 96.30% | 0.00% | 0.00% | 3.73% | NA |
| VI/Aromatic | 96 | 38.50% | 0.00% | 26.04% | 35.42% | NA |
| Intermediate | 90 | 53.30% | 1.10% | 6.67% | 38.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1101255638 | C -> T | LOC_Os11g03330.1 | downstream_gene_variant ; 1658.0bp to feature; MODIFIER | silent_mutation | Average:6.708; most accessible tissue: Minghui63 flag leaf, score: 11.122 | N | N | N | N |
| vg1101255638 | C -> T | LOC_Os11g03340.1 | intron_variant ; MODIFIER | silent_mutation | Average:6.708; most accessible tissue: Minghui63 flag leaf, score: 11.122 | N | N | N | N |
| vg1101255638 | C -> DEL | N | N | silent_mutation | Average:6.708; most accessible tissue: Minghui63 flag leaf, score: 11.122 | N | N | N | N |