PairsQC Report
Summary table

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 4DNFIN5DX6QZ
Total reads 230,610,382
Short cis reads (<20kb) 71,905,701
Cis reads (>20kb) 141,373,073
Trans reads 17,331,608
Cis/Trans ratio 89.079
% Long-range intrachromosomal reads 61.304
convergence Good
slope -1
Proportion of read orientation versus genomic separation

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 : 4DNFIN5DX6QZ

Contact probability versus genomic separation

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 : 4DNFIN5DX6QZ

Contact probability versus genomic separation, per chromosome

Interactive Figure 1. Contact probability versus genomic separation, per chromosome : 4DNFIN5DX6QZ

References
[1] Rao et al., A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping, Cell 159:7:1665-1680 (2014)
[2] Imakaev et al., Iterative correction of Hi-C data reveals hallmarks of chromosome organization, Nature Methods 9:10:999-1003 (2012)
[3] Sanborn et al., Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genome, Proc. Natl. Acad. Sci. USA 112:47:E6456-E6465 (2015)