The following table shows important quality control metrics for each sample.
Gene Length (bp): The total number of base pairs (bp) in the gene annotation.
Total reads: The total number of reads mapping to the gene of interest in the database across all 6
replicates.
Mean Coverage: The mean read depth computed across all gene bases.
Coverage Coefficient of Variation (CV): The ratio of the standard deviation of read depth to the mean read
depth,
a measure of relative variability of coverage across all gene bases.
Coverage uniformity: The percentage of gene bases with more than 20% of the mean coverage.
% Bases with coverage > XXXx: The percentage of gene bases with coverage > 1000x/500x/300x/160x. Note that
parts of the selected isoform may not be expressed in the sample, therby falsely lowering these scores. Also
check the gene coverage plot.
FPKM: The number of fragments mapping to the gene of interest, per kilobase of gene, per million.
Gene | Gene Length (bp) | Total Reads | Mean Coverage | Coverage CV | Coverage Uniformity | % Bases with coverage > 1000x | % Bases with coverage > 500x | % Bases with coverage > 300x | % Bases with coverage > 160x | FPKM |
---|---|---|---|---|---|---|---|---|---|---|
GENEX | 1,285 | 516,729 | 7,323 | 0.16 | 100.0% | 100.0% | 100.0% | 100.0% | 100.0% | 1,288.08 |
The following plots show coverage in the eSHAPE db-K562 for the gene of interest. A sudden drop in coverage, especially at the 3’ and 5’ UTRs, might indicate expression of a shorter isoform in the sample. Dips in coverage, for the most part, are at exon edges.