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.

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.

The following plots show mutation line plots across the gene of interest. Corresponding spikes in mutation, found in NAI and DMSO samples, might indicate a SNP in the sample compared to the reference genome.

The following box plot shows mutation rate distributions for DMSO and NAI samples for the gene of interest.

The following plot shows SHAPE reactivity scores across the gene of interest at each position with >300x coverage. Higher reactivity scores correlate with a higher likelihood of being unpaired.

The following table outlines the data files delivered with this eSHAPE db gene package.