| Variant ID: vg1101255640 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 1255640 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
GTTCGTGATCGGAACATTACTCCGGTCAAAGTGAAGAAATGGTCAGACATTAGTAACACAGAGCAGGAACACATATTTGCCTCGATTACGGTACGCATCT[A/G]
TCTTCCTATGAAATGTTCTCTCTTGTTTTCAATAAAACTATGCTTGCACTGAATCATTTGTTTTTATAATTTTGCAGGACAAGTTTGAAAATGAAGATCC
GGATCTTCATTTTCAAACTTGTCCTGCAAAATTATAAAAACAAATGATTCAGTGCAAGCATAGTTTTATTGAAAACAAGAGAGAACATTTCATAGGAAGA[T/C]
AGATGCGTACCGTAATCGAGGCAAATATGTGTTCCTGCTCTGTGTTACTAATGTCTGACCATTTCTTCACTTTGACCGGAGTAATGTTCCGATCACGAAC
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 44.20% | 0.30% | 4.68% | 50.91% | NA |
| All Indica | 2759 | 12.30% | 0.30% | 6.05% | 81.33% | NA |
| All Japonica | 1512 | 97.60% | 0.00% | 0.33% | 2.12% | NA |
| Aus | 269 | 69.90% | 0.70% | 5.95% | 23.42% | NA |
| Indica I | 595 | 12.80% | 0.00% | 8.07% | 79.16% | NA |
| Indica II | 465 | 7.30% | 0.60% | 4.52% | 87.53% | NA |
| Indica III | 913 | 8.40% | 0.30% | 4.71% | 86.53% | NA |
| Indica Intermediate | 786 | 19.30% | 0.40% | 7.00% | 73.28% | 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% | 8.89% | 36.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1101255640 | A -> DEL | N | N | silent_mutation | Average:6.708; most accessible tissue: Minghui63 flag leaf, score: 11.122 | N | N | N | N |
| vg1101255640 | A -> G | LOC_Os11g03330.1 | downstream_gene_variant ; 1660.0bp to feature; MODIFIER | silent_mutation | Average:6.708; most accessible tissue: Minghui63 flag leaf, score: 11.122 | N | N | N | N |
| vg1101255640 | A -> G | LOC_Os11g03340.1 | intron_variant ; MODIFIER | silent_mutation | Average:6.708; most accessible tissue: Minghui63 flag leaf, score: 11.122 | N | N | N | N |