Bismark report for: /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-127_S33_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-127_S33_L005_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 --ignore-quals --no-mixed --no-discordant --dovetail --minins 60 --maxins 500
Option '--non_directional' specified: alignments to all strands were being performed (OT, OB, CTOT, CTOB)

Final Alignment report
======================
Sequence pairs analysed in total:	22262118
Number of paired-end alignments with a unique best hit:	14621941
Mapping efficiency:	65.7% 
Sequence pairs with no alignments under any condition:	3637096
Sequence pairs did not map uniquely:	4003081
Sequence pairs which were discarded because genomic sequence could not be extracted:	46947

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	6867884	((converted) top strand)
GA/CT/CT:	336289	(complementary to (converted) top strand)
GA/CT/GA:	343587	(complementary to (converted) bottom strand)
CT/GA/GA:	7027234	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	472905546

Total methylated C's in CpG context:	13785497
Total methylated C's in CHG context:	2368598
Total methylated C's in CHH context:	15913566
Total methylated C's in Unknown context:	537770


Total unmethylated C's in CpG context:	53596547
Total unmethylated C's in CHG context:	95024861
Total unmethylated C's in CHH context:	292216477
Total unmethylated C's in Unknown context:	2344027


C methylated in CpG context:	20.5%
C methylated in CHG context:	2.4%
C methylated in CHH context:	5.2%
C methylated in unknown context (CN or CHN):	18.7%


Bismark completed in 0d 6h 43m 36s