Bismark report for: /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-167_S10_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-167_S10_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/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:	24481250
Number of paired-end alignments with a unique best hit:	10412084
Mapping efficiency:	42.5% 
Sequence pairs with no alignments under any condition:	12046556
Sequence pairs did not map uniquely:	2022610
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:	5155290	((converted) top strand)
GA/CT/CT:	0	(complementary to (converted) top strand)
GA/CT/GA:	0	(complementary to (converted) bottom strand)
CT/GA/GA:	5256794	((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:	326275224

Total methylated C's in CpG context:	12338296
Total methylated C's in CHG context:	2041015
Total methylated C's in CHH context:	6293950
Total methylated C's in Unknown context:	65243


Total unmethylated C's in CpG context:	31811465
Total unmethylated C's in CHG context:	67746920
Total unmethylated C's in CHH context:	206043578
Total unmethylated C's in Unknown context:	702416


C methylated in CpG context:	27.9%
C methylated in CHG context:	2.9%
C methylated in CHH context:	3.0%
C methylated in unknown context (CN or CHN):	8.5%


Bismark completed in 0d 0h 50m 51s