Cis-to-trans ratio is computed as the ratio of long-range cis reads (>20kb) to trans reads plus long-range cis reads. Typically, cis-to-trans ratio higher than 40% is required. Percentage of long-range cis reads is the ratio of long-range cis reads to total number of reads. Minimum 15% is required and 40% or higher suggests a good library[1]. Convergence is determined as standard deviation of proportions of four read orientations to be <0.002 (Very good) or <0.05 (Good) (See below section Proportion of read orientation versus genomic separation). The slope of log10 contact probability vs distance between 10kb ~ 300kb representing TAD is also provided as well. (See below section Contact probability versus genomic separation.)
Table 1. Summary Table
| QC field | 4DNFIFQC43YQ |
|---|---|
| Total reads | 908,931,684 |
| Short cis reads (<20kb) | 152,581,959 |
| Cis reads (>20kb) | 506,930,453 |
| Trans reads | 249,419,272 |
| Cis/Trans ratio | 67.023 |
| % Long-range intrachromosomal reads | 55.772 |
| convergence | Very Good |
| slope | -0.78 |
Contact frequency (number of reads, left) and proportion of reads (right) are shown, stratified by read orientation. Good four-cutter and six-cutter samples would converge at ~3kb (10^3.5) and ~30kb (10^4.5), respectively[1]. Convergence is determined by the standard deviation of the proportions being less than 0.005.
Figure 1. Get High-res Image Proportion of read orientation versus genomic separation : 4DNFIFQC43YQ
Contact probability (number of reads, normalized by number of bins and bin size) is shown with respect to genomic separation between mates[2][3]. The slope between distance 10kb ~ 300kb (10^4 ~ 10^5.5) representing a TAD is calculated. A good mitotic sample would have a slope close to ~ -0.76[3].
Figure 2. Get High-res Image Contact probability versus genomic separation : 4DNFIFQC43YQ
Interactive Figure 1. Contact probability versus genomic separation, per chromosome : 4DNFIFQC43YQ