eSHAPE db-K562 Report

invitro GENEX


Gene Metrics Table

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

Coverage Plot: invitro GENEX

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.