| Variant ID: vg0103668423 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr01 | Position: 3668423 |
| Reference Allele: A | Alternative Allele: AAG |
| Primary Allele: A | Secondary Allele: AAG |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 295. )
TACTCAACAAAAAAAAGGCAAAAAAGATCCTGAGAATGACATACAGACTTGTCAAAAAAAAGCTCTATGACGGACGAAACAAAAGGACATATCACAACAA[A/AAG]
CTGAGTGGACATATAAAGCATATTTATGGCCCTTGGGAGGCATTGAAGGAGAGATGTATCTGGTACTGTTAATAATGAGATATTACGAGGAACAAGGTAT
ATACCTTGTTCCTCGTAATATCTCATTATTAACAGTACCAGATACATCTCTCCTTCAATGCCTCCCAAGGGCCATAAATATGCTTTATATGTCCACTCAG[T/CTT]
TTGTTGTGATATGTCCTTTTGTTTCGTCCGTCATAGAGCTTTTTTTTGACAAGTCTGTATGTCATTCTCAGGATCTTTTTTGCCTTTTTTTTGTTGAGTA
| Populations | Population Size | Frequency of A(primary allele) | Frequency of AAG(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.20% | 0.70% | 0.04% | 0.00% | NA |
| All Indica | 2759 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 65.60% | 32.30% | 2.08% | 0.00% | NA |
| Intermediate | 90 | 98.90% | 1.10% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0103668423 | A -> AAG | LOC_Os01g07620.1 | upstream_gene_variant ; 2378.0bp to feature; MODIFIER | silent_mutation | Average:42.591; most accessible tissue: Minghui63 flower, score: 70.218 | N | N | N | N |
| vg0103668423 | A -> AAG | LOC_Os01g07610.1 | downstream_gene_variant ; 4105.0bp to feature; MODIFIER | silent_mutation | Average:42.591; most accessible tissue: Minghui63 flower, score: 70.218 | N | N | N | N |
| vg0103668423 | A -> AAG | LOC_Os01g07630.1 | intron_variant ; MODIFIER | silent_mutation | Average:42.591; most accessible tissue: Minghui63 flower, score: 70.218 | N | N | N | N |