Bismark report for: /gscratch/srlab/strigg/data/Pgenr/FASTQS/20bp_clip/EPI-167_S10_L002_R1_001_val_1.20bp-trim.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/20bp_clip/EPI-167_S10_L002_R2_001_val_2.20bp-trim.fq.gz (version: v0.19.0)
Bismark was run with Bowtie 2 against the bisulfite genome of /gscratch/srlab/strigg/data/Pgenr/OFS/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --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:	24477306
Number of paired-end alignments with a unique best hit:	10276418
Mapping efficiency:	42.0% 
Sequence pairs with no alignments under any condition:	11771224
Sequence pairs did not map uniquely:	2429664
Sequence pairs which were discarded because genomic sequence could not be extracted:	0

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	5086774	((converted) top strand)
GA/CT/CT:	0	(complementary to (converted) top strand)
GA/CT/GA:	0	(complementary to (converted) bottom strand)
CT/GA/GA:	5189644	((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:	256660837

Total methylated C's in CpG context:	8579400
Total methylated C's in CHG context:	1100210
Total methylated C's in CHH context:	4713706
Total methylated C's in Unknown context:	34055


Total unmethylated C's in CpG context:	24327012
Total unmethylated C's in CHG context:	52134228
Total unmethylated C's in CHH context:	165806281
Total unmethylated C's in Unknown context:	540239


C methylated in CpG context:	26.1%
C methylated in CHG context:	2.1%
C methylated in CHH context:	2.8%
C methylated in unknown context (CN or CHN):	5.9%


Bismark completed in 0d 0h 43m 57s