EMUMADZ Variant Analysis Viewer
File Landing Page
| Sample Name | Action | Sample ID | Lab ID | File Name | Size | Modified |
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| Loading available files... | ||||||
Please submit an issue here if you experience any bugs or have a feature request. In both cases please provide as much information as possible (e.g. steps taken to reproduce a problem). If the issue is visual, screenshots will be very helpful.
Sample Analysis Overview
This table displays annotated variants from your sample with both VEP and SnpEff predictions. Use the filters above to narrow results by chromosome, impact level, gene name, or sequencing depth. Click "IGV" to visualize variants in context with BAM alignments. "Gosling" functionality is currently not enabled.
| Variant ID | Actions | Genotype
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Genotype explanation:
• 0/0: Homozygous to reference • 0/1: Heterozygous reference/Homozygous mutant • 1/0: Homozygous reference/Heterozygous mutant • 1/1: Homozygous to mutant Note that filters have been intentionally loosened. In this case, this means a homozygosity call will be made if 85% of reads have the same SNP (or lack of). |
Depth
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Read depth:
The number of reads factored into homozygosity calculations. You may see more (but not less) reads than this number on the IGV genome browser. This is not an error, the data file displays all reads, including those that are low quality for visualisation purposes. |
AF
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Allele frequencies:
• 0.0: 0 mutant alleles • 0.5: Half (1) mutant allele(s) • 1.0: All mutant alleles Note that in this case, allele frequencies are genotype based (Mendelian genetics) and not read based (i.e. not interpreted as a proportion of reads). |
VEP Gene
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Gene as recorded in VEP database.
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SnpEff Gene
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Gene as recorded in SnpEff database.
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VEP Impact
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Impact of modification as recorded in VEP database.
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SnpEff Impact
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Impact of modification as recorded in SnpEff database.
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VEP Consequence
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Description of modification as recorded in VEP database.
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SnpEff Effect
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Description of modification as recorded in SnpEff database.
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| Load a JSON file to view variants | ||||||||||
Important information
- Note that the tracks shown may not always appear to conform to your filters for genotype, depth and allele frequency.
- This is not an error. The tracks include reads of all quality levels by design to provide the maximum possible level of information.
- Clicking on the individual reads will yield more information on mapping quality and other read-specific information.
- Note that reads with low mapping quality or phred score were naturally excluded from the allele frequency calculations, even if they appear on the tracks. The custom genome annotation coordinates reflects the zebrafish genome assembly Zv9 only. Newer genome versions are provided for testing purposes only and should not be used for this experiment. Automated checks for annotation file compatibility will be implemented later.
- Homozygosity mapping plots are not yet implemented and will arrive in a future update.
Troubleshooting
- If this is blank the first time you click on this IGV browser tab, this is not an error. We first need to initialise IGV by clicking the link in the Variant Table tab.
- If anything unexpected happens, refreshing IGV or the site itself may work.
IGV information
- The IGV browser below embeds IGV internally. All features associated with IGV will be the same.
- The first track shows a high level homozygosity map. This is intended for viewing at a
chromosome or genome-wide scale to identify mutation hotspots. - All other tracks show a low level alignment view. This is intended for viewing at a
single-nucleotide resolution to examine individual SNPs. - Red colour of the read indicates a forward strand, while blue indicates a reverse strand.
- Lighter coloured reads indicate lower quality, darker is better.
- Our variant caller applied a mapping quality (MAPQ) threshold of 20 == 99% probability that the read is mapped accurately.
- Our variant caller applied a base quality (phred) threshold of 20 == 99% probability that the base is called correctly.
- These thresholds are generally recommended as a baseline for SNP discovery and used as defaults by most variant callers.
- You will still see reads not matching these criteria, as the bam file shows all information by design. However, the filtering has been correctly applied in allele frequency calculations.
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