| Variant ID: vg1200352075 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr12 | Position: 352075 |
| Reference Allele: CA | Alternative Allele: C |
| Primary Allele: CA | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
ATATCTAAAATCGTGTGTAGAACTATCAGCTAGGTGGGTCAAGTGCCACATTTTTTGTCGTGTTTTTATGTATTCATCTTGATGTATATTACTATTACTT[CA/C]
AAAATGTTTCCAGACCTATTCTATGTGCTTTATTAGTCAAGTTTTCAGCTGATAATAAGGAATCAAAACAACAGTCCTTGATCAATGTGTGAATATGAAG
CTTCATATTCACACATTGATCAAGGACTGTTGTTTTGATTCCTTATTATCAGCTGAAAACTTGACTAATAAAGCACATAGAATAGGTCTGGAAACATTTT[TG/G]
AAGTAATAGTAATATACATCAAGATGAATACATAAAAACACGACAAAAAATGTGGCACTTGACCCACCTAGCTGATAGTTCTACACACGATTTTAGATAT
| Populations | Population Size | Frequency of CA(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 56.60% | 43.20% | 0.25% | 0.00% | NA |
| All Indica | 2759 | 33.50% | 66.20% | 0.36% | 0.00% | NA |
| All Japonica | 1512 | 96.20% | 3.70% | 0.07% | 0.00% | NA |
| Aus | 269 | 50.20% | 49.40% | 0.37% | 0.00% | NA |
| Indica I | 595 | 47.40% | 52.40% | 0.17% | 0.00% | NA |
| Indica II | 465 | 18.10% | 81.30% | 0.65% | 0.00% | NA |
| Indica III | 913 | 35.80% | 64.10% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 29.30% | 70.10% | 0.64% | 0.00% | NA |
| Temperate Japonica | 767 | 94.70% | 5.30% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 97.40% | 2.40% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.80% | 1.20% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 97.90% | 2.10% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 73.30% | 26.70% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1200352075 | CA -> C | LOC_Os12g01574.1 | upstream_gene_variant ; 1431.0bp to feature; MODIFIER | silent_mutation | Average:58.27; most accessible tissue: Minghui63 flag leaf, score: 79.676 | N | N | N | N |
| vg1200352075 | CA -> C | LOC_Os12g01570.1 | downstream_gene_variant ; 2931.0bp to feature; MODIFIER | silent_mutation | Average:58.27; most accessible tissue: Minghui63 flag leaf, score: 79.676 | N | N | N | N |
| vg1200352075 | CA -> C | LOC_Os12g01590.1 | downstream_gene_variant ; 3447.0bp to feature; MODIFIER | silent_mutation | Average:58.27; most accessible tissue: Minghui63 flag leaf, score: 79.676 | N | N | N | N |
| vg1200352075 | CA -> C | LOC_Os12g01580.1 | intron_variant ; MODIFIER | silent_mutation | Average:58.27; most accessible tissue: Minghui63 flag leaf, score: 79.676 | N | N | N | N |
| vg1200352075 | CA -> C | LOC_Os12g01580.2 | intron_variant ; MODIFIER | silent_mutation | Average:58.27; most accessible tissue: Minghui63 flag leaf, score: 79.676 | N | N | N | N |