Bismark report for: /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-159_S6_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-159_S6_L002_R2_001_val_2.fq.gz (version: v0.19.0)
Bismark was run with Bowtie 2 against the bisulfite genome of /gscratch/srlab/strigg/data/Pgenr/ with the specified options: -q --score-min L,0,-1.2 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --minins 60 --maxins 500
Option '--directional' specified (default mode): alignments to complementary strands (CTOT, CTOB) were ignored (i.e. not performed)

Final Alignment report
======================
Sequence pairs analysed in total:	15453987
Number of paired-end alignments with a unique best hit:	9136462
Mapping efficiency:	59.1% 
Sequence pairs with no alignments under any condition:	3665126
Sequence pairs did not map uniquely:	2652399
Sequence pairs which were discarded because genomic sequence could not be extracted:	55159

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	4472321	((converted) top strand)
GA/CT/CT:	0	(complementary to (converted) top strand)
GA/CT/GA:	0	(complementary to (converted) bottom strand)
CT/GA/GA:	4608982	((converted) bottom strand)

Number of alignments to (merely theoretical) complementary strands being rejected in total:	0

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	289174054

Total methylated C's in CpG context:	9492162
Total methylated C's in CHG context:	1624273
Total methylated C's in CHH context:	9702386
Total methylated C's in Unknown context:	300927


Total unmethylated C's in CpG context:	31891715
Total unmethylated C's in CHG context:	60744506
Total unmethylated C's in CHH context:	175719012
Total unmethylated C's in Unknown context:	1466391


C methylated in CpG context:	22.9%
C methylated in CHG context:	2.6%
C methylated in CHH context:	5.2%
C methylated in unknown context (CN or CHN):	17.0%


Bismark completed in 0d 3h 27m 22s