| Variant ID: vg0315011654 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr03 | Position: 15011654 |
| Reference Allele: CAACGGCGTCATCTATTAAAA | Alternative Allele: TAACGGCGTCATCTATTAAAA,C |
| Primary Allele: CAACGGCGTCATCTATTAAA A | Secondary Allele: TAACGGCGTCATCTATTAAA A |
Inferred Ancestral Allele: Not determined.
ACTTAAAGTATTATGAGTAATAAAACAACTCATAACAAAATAAATTACAATTACGTAAATTTTTTGAATAAGACAAATGGTCAAACATGTGAGAAAAAGT[CAACGGCGTCATCTATTAAAA/TAACGGCGTCATCTATTAAAA,C]
AAACGGAGGTAGTATGTTATTCCCTTTTCTGCATCCATGATAGATATTGCCTCTGGTTTTAAATGGACAAATCGGACGTCTGGCATTTCTCAGAACATCG
CGATGTTCTGAGAAATGCCAGACGTCCGATTTGTCCATTTAAAACCAGAGGCAATATCTATCATGGATGCAGAAAAGGGAATAACATACTACCTCCGTTT[TTTTAATAGATGACGCCGTTG/TTTTAATAGATGACGCCGTTA,G]
ACTTTTTCTCACATGTTTGACCATTTGTCTTATTCAAAAAATTTACGTAATTGTAATTTATTTTGTTATGAGTTGTTTTATTACTCATAATACTTTAAGT
| Populations | Population Size | Frequency of CAACGGCGTCATCTATTAAA A(primary allele) | Frequency of TAACGGCGTCATCTATTAAA A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 92.00% | 5.30% | 2.20% | 0.00% | C: 0.53% |
| All Indica | 2759 | 87.00% | 8.70% | 3.41% | 0.00% | C: 0.87% |
| All Japonica | 1512 | 99.40% | 0.10% | 0.46% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 94.80% | 0.30% | 4.20% | 0.00% | C: 0.67% |
| Indica II | 465 | 70.80% | 20.60% | 6.88% | 0.00% | C: 1.72% |
| Indica III | 913 | 95.70% | 3.60% | 0.55% | 0.00% | C: 0.11% |
| Indica Intermediate | 786 | 80.70% | 13.90% | 4.07% | 0.00% | C: 1.40% |
| Temperate Japonica | 767 | 99.70% | 0.10% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 99.00% | 0.20% | 0.79% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.00% | 0.83% | 0.00% | NA |
| VI/Aromatic | 96 | 96.90% | 3.10% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 90.00% | 5.60% | 3.33% | 0.00% | C: 1.11% |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0315011654 | CAACGGCGTCATCTATTAAAA -> C | LOC_Os03g26240.1 | upstream_gene_variant ; 2202.0bp to feature; MODIFIER | silent_mutation | Average:38.71; most accessible tissue: Minghui63 panicle, score: 62.157 | N | N | N | N |
| vg0315011654 | CAACGGCGTCATCTATTAAAA -> C | LOC_Os03g26260.1 | upstream_gene_variant ; 4151.0bp to feature; MODIFIER | silent_mutation | Average:38.71; most accessible tissue: Minghui63 panicle, score: 62.157 | N | N | N | N |
| vg0315011654 | CAACGGCGTCATCTATTAAAA -> C | LOC_Os03g26229.1 | downstream_gene_variant ; 3395.0bp to feature; MODIFIER | silent_mutation | Average:38.71; most accessible tissue: Minghui63 panicle, score: 62.157 | N | N | N | N |
| vg0315011654 | CAACGGCGTCATCTATTAAAA -> C | LOC_Os03g26250.1 | intron_variant ; MODIFIER | silent_mutation | Average:38.71; most accessible tissue: Minghui63 panicle, score: 62.157 | N | N | N | N |
| vg0315011654 | CAACGGCGTCATCTATTAAAA -> TAACGGCGTCATCTATTAAAA | LOC_Os03g26240.1 | upstream_gene_variant ; 2201.0bp to feature; MODIFIER | silent_mutation | Average:38.71; most accessible tissue: Minghui63 panicle, score: 62.157 | N | N | N | N |
| vg0315011654 | CAACGGCGTCATCTATTAAAA -> TAACGGCGTCATCTATTAAAA | LOC_Os03g26260.1 | upstream_gene_variant ; 4152.0bp to feature; MODIFIER | silent_mutation | Average:38.71; most accessible tissue: Minghui63 panicle, score: 62.157 | N | N | N | N |
| vg0315011654 | CAACGGCGTCATCTATTAAAA -> TAACGGCGTCATCTATTAAAA | LOC_Os03g26229.1 | downstream_gene_variant ; 3394.0bp to feature; MODIFIER | silent_mutation | Average:38.71; most accessible tissue: Minghui63 panicle, score: 62.157 | N | N | N | N |
| vg0315011654 | CAACGGCGTCATCTATTAAAA -> TAACGGCGTCATCTATTAAAA | LOC_Os03g26250.1 | intron_variant ; MODIFIER | silent_mutation | Average:38.71; most accessible tissue: Minghui63 panicle, score: 62.157 | N | N | N | N |