PΨFinder: a practical tool for the identification and visualization of novel pseudogenes in DNA sequencing data

BMC Bioinformatics

Table 1 Summary of identified processed pseudogene candidates across all samples analyzed

Predicted PΨg	Number of samples predicted to harbor the PΨg (N = 218)	Number of predicted PΨg-insertion sites, according to its insert site location^a
		Exonic			Intronic			Intergenic
		CP-CR^b	CP	CR	CP-CR	CP	CR	CP-CR	CP	CR
CBX3^c	180 (82.6%)	0	0	0	123	3	59	0	0	0
BMPR1A	155 (71.1%)	0	5	1	0	321	99	1	320	134
PTEN	51 (23.4%)	0	1	1	0	131	27	0	151	39
DHFR	29 (13.3%)	0	0	0	0	39	8	0	17	6
HNRNPC	6 (2.8%)	0	0	0	0	0	0	3	1	2
POLE	1 (0.5%)	0	0	0	0	2	0	0	1	1
SMAD4^c	1 (0.5%)	0	0	0	1	0	0	0	1	0

^aNote that the sum of the predicted PΨg-insertion sites across different regions may vary from the total amount of samples, since one predicted PΨg may be predicted to have several insertion sites
^bCP and CR stand for Chimeric Pair and Chimeric Read respectively. CP–CR denotes evidence from both Chimeric Pairs and Chimeric Reads supporting the insertion site, while the columns CP and CR denote only one type of chimeric evidence
^cSelected PΨgs for experimental validation

ISSN: 1471-2105