Bismark report for: /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-41_S38_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-41_S38_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 -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:	25055317
Number of paired-end alignments with a unique best hit:	13533998
Mapping efficiency:	54.0% 
Sequence pairs with no alignments under any condition:	7395470
Sequence pairs did not map uniquely:	4125849
Sequence pairs which were discarded because genomic sequence could not be extracted:	82651

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	6694793	((converted) top strand)
GA/CT/CT:	0	(complementary to (converted) top strand)
GA/CT/GA:	0	(complementary to (converted) bottom strand)
CT/GA/GA:	6756554	((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:	410166096

Total methylated C's in CpG context:	15066999
Total methylated C's in CHG context:	2345442
Total methylated C's in CHH context:	13871302
Total methylated C's in Unknown context:	474040


Total unmethylated C's in CpG context:	43389569
Total unmethylated C's in CHG context:	86494843
Total unmethylated C's in CHH context:	248997941
Total unmethylated C's in Unknown context:	2036332


C methylated in CpG context:	25.8%
C methylated in CHG context:	2.6%
C methylated in CHH context:	5.3%
C methylated in unknown context (CN or CHN):	18.9%


Bismark completed in 0d 5h 5m 13s