Bismark report for: /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-103_S27_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-103_S27_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:	20349659
Number of paired-end alignments with a unique best hit:	13364383
Mapping efficiency:	65.7% 
Sequence pairs with no alignments under any condition:	3385894
Sequence pairs did not map uniquely:	3599382
Sequence pairs which were discarded because genomic sequence could not be extracted:	45055

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	6344954	((converted) top strand)
GA/CT/CT:	288878	(complementary to (converted) top strand)
GA/CT/GA:	294928	(complementary to (converted) bottom strand)
CT/GA/GA:	6390568	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	436619499

Total methylated C's in CpG context:	12108570
Total methylated C's in CHG context:	2075398
Total methylated C's in CHH context:	14520988
Total methylated C's in Unknown context:	485587


Total unmethylated C's in CpG context:	48927920
Total unmethylated C's in CHG context:	89229392
Total unmethylated C's in CHH context:	269757231
Total unmethylated C's in Unknown context:	2195501


C methylated in CpG context:	19.8%
C methylated in CHG context:	2.3%
C methylated in CHH context:	5.1%
C methylated in unknown context (CN or CHN):	18.1%


Bismark completed in 0d 6h 36m 43s