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QC Dashboard

Raw Fastq Metrics

Sequence Depth & Quality

Raw fastqs were used to calculcate the mean sequencing depth per sample (Sample Coverage), the median quality scores for each sample, and the sequence quality per base for each sample. Note that quality scores above 25 are generally considered acceptable, and that on Illumina sequencers quality scores always decrease toward the end of the read.

Sample Coverage

Median Quality Scores

Per Base Sequence Quality

Quality Scores Heatmap

Sequence Metrics

GC content was also calculated based on the raw fastqs.

GC Content

Post Trimming/QC Fastq Metrics

Sequence Depth & Quality

Trimmed and quality-filtered fastqs were used to calculate the mean sequencing depth per sample (Sample Coverage), the median quality scores for each sample, and the sequence quality per base for each sample. Note that quality scores above 25 are generally considered acceptable, and that on Illumina sequencers quality scores always decrease toward the end of the read.

Sample Coverage

Median Quality Scores

Per Base Sequence Quality

Quality Scores Heatmap

Sequence Metrics

The following metrics were also generated based on the trimmed and filtered fastqs: length distributions and GC content.

Read Length Distributions

GC Content


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