Resequencing
The Resequencing workflow compares the DNA sequence in the sample(s) against a reference genome and identifies any variants (SNPs or indels) relative to the reference sequence. The main output files generated by the Resequencing workflow are .bam files (containing the aligned reads) and .vcf files (containing the variant calls).
Resequencing page provides four graphs, described below.
Low Percentage refers to run statistics that should be near 0 for an ideal run.
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y-axis |
x-axis |
Description |
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Percent |
Mismatch 1 |
The average percentage of mismatches for Read 1 over all cycles. |
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Mismatch 2 |
The average percentage of mismatches for Read 2 over all cycles. |
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Phasing 1 |
The percentage of molecules that fall behind (fail to incorporate a base) in a sequencing cycle in Read 1. |
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Phasing 2 |
The percentage of molecules that fall behind (fail to incorporate a base) in a sequencing cycle in Read 2. |
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PrePhasing 1 |
The percentage of molecules that run ahead (incorporate an extra base) in a sequencing cycle in Read 1. |
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PrePhasing 2 |
The percentage of molecules that run ahead (incorporate an extra base) in a sequencing cycle in Read 2. |
High Percentage refers to run statistics that should all be close to 100% for a good run.
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y-axis |
x-axis |
Description |
|---|---|---|
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Percent |
|20/|1 1 |
The ratio of intensities at cycle 20 to the intensities at cycle 1 for Read 1. |
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|20/|1 2 |
The ratio of intensities at cycle 20 to the intensities at cycle 1 for Read 2. |
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Align 1 |
The percentage of clusters that aligned to the reference in Read 1. |
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Align 2 |
The percentage of clusters that aligned to the reference in Read 2. |
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PE Orientation |
The percentage of paired-end alignments with the expected orientation. |
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PE Resynthesis |
The ratio of first cycle intensities for Read 1 to first cycle intensities for Read 2. |
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PF |
The percentage of clusters passing filters. |
A cluster represents a clonal spot on the flow cell that contains the amplified DNA strands that will be sequenced.
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y-axis |
x-axis |
Description |
|---|---|---|
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Clusters |
Raw |
The total number of clusters detected in the run. |
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PF |
The total number of clusters passing filter in the run. |
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Unaligned |
The total number of clusters passing filter that did not align to the reference genome, if applicable. Clusters that are unindexed are not included in the unaligned count. |
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Unindexed |
The total number of clusters passing filter that were not associated with any index sequence in the run. |
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Duplicate |
The total number of clusters for a paired-end sequencing run which are considered to be PCR duplicates. |
Mismatch refers to any mismatch between sequence read and a reference genome after alignment.
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y-axis |
x-axis |
Description |
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Percent |
Cycle |
Plots the % mismatches for all clusters in a run versus cycle |