| Variant ID: vg0517887386 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr05 | Position: 17887386 |
| Reference Allele: TA | Alternative Allele: T,TAA |
| Primary Allele: T | Secondary Allele: TA |
Inferred Ancestral Allele: Not determined.
TGAGACCTGCAAATAAAAAAGAATTTATAATTCACGTCAACAAAGCAATCCTTGTGACTCAGAGGAGGCTCAGGATATGCAGATGACTCAAACCAGCAAA[TA/T,TAA]
AAAAAAAATTATACTACTTATTACTTAATGTCTCCAAAGCAATTAGATAACTCACTTATGTTATTACCTTTAGCTGCTCCAATGGCTATTGAGAGCCTTT
AAAGGCTCTCAATAGCCATTGGAGCAGCTAAAGGTAATAACATAAGTGAGTTATCTAATTGCTTTGGAGACATTAAGTAATAAGTAGTATAATTTTTTTT[TA/A,TTA]
TTTGCTGGTTTGAGTCATCTGCATATCCTGAGCCTCCTCTGAGTCACAAGGATTGCTTTGTTGACGTGAATTATAAATTCTTTTTTATTTGCAGGTCTCA
| Populations | Population Size | Frequency of T(primary allele) | Frequency of TA(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 64.80% | 34.90% | 0.28% | 0.00% | TAA: 0.06% |
| All Indica | 2759 | 94.20% | 5.60% | 0.22% | 0.00% | NA |
| All Japonica | 1512 | 9.10% | 90.50% | 0.26% | 0.00% | TAA: 0.07% |
| 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 | 74.40% | 24.90% | 0.65% | 0.00% | NA |
| Indica III | 913 | 99.30% | 0.50% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 95.50% | 4.20% | 0.25% | 0.00% | NA |
| Temperate Japonica | 767 | 3.00% | 96.90% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 21.60% | 78.20% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 2.50% | 96.30% | 0.83% | 0.00% | TAA: 0.41% |
| VI/Aromatic | 96 | 7.30% | 92.70% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 53.30% | 41.10% | 3.33% | 0.00% | TAA: 2.22% |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0517887386 | TA -> T | LOC_Os05g30830.1 | downstream_gene_variant ; 4582.0bp to feature; MODIFIER | silent_mutation | Average:48.457; most accessible tissue: Callus, score: 67.262 | N | N | N | N |
| vg0517887386 | TA -> T | LOC_Os05g30820.1 | intron_variant ; MODIFIER | silent_mutation | Average:48.457; most accessible tissue: Callus, score: 67.262 | N | N | N | N |
| vg0517887386 | TA -> T | LOC_Os05g30820.2 | intron_variant ; MODIFIER | silent_mutation | Average:48.457; most accessible tissue: Callus, score: 67.262 | N | N | N | N |
| vg0517887386 | TA -> TAA | LOC_Os05g30830.1 | downstream_gene_variant ; 4581.0bp to feature; MODIFIER | silent_mutation | Average:48.457; most accessible tissue: Callus, score: 67.262 | N | N | N | N |
| vg0517887386 | TA -> TAA | LOC_Os05g30820.1 | intron_variant ; MODIFIER | silent_mutation | Average:48.457; most accessible tissue: Callus, score: 67.262 | N | N | N | N |
| vg0517887386 | TA -> TAA | LOC_Os05g30820.2 | intron_variant ; MODIFIER | silent_mutation | Average:48.457; most accessible tissue: Callus, score: 67.262 | N | N | N | N |