Bismark report for: EPI-167_S10_L002_R1_001_val_1.fq.gz and 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:	23436512
Number of paired-end alignments with a unique best hit:	9588745
Mapping efficiency:	40.9% 
Sequence pairs with no alignments under any condition:	11082779
Sequence pairs did not map uniquely:	2764988
Sequence pairs which were discarded because genomic sequence could not be extracted:	1

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	4754776	((converted) top strand)
GA/CT/CT:	0	(complementary to (converted) top strand)
GA/CT/GA:	0	(complementary to (converted) bottom strand)
CT/GA/GA:	4833968	((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:	199524252

Total methylated C's in CpG context:	6315385
Total methylated C's in CHG context:	695740
Total methylated C's in CHH context:	3620104
Total methylated C's in Unknown context:	18796


Total unmethylated C's in CpG context:	18667755
Total unmethylated C's in CHG context:	40114533
Total unmethylated C's in CHH context:	130110735
Total unmethylated C's in Unknown context:	361000


C methylated in CpG context:	25.3%
C methylated in CHG context:	1.7%
C methylated in CHH context:	2.7%
C methylated in unknown context (CN or CHN):	4.9%


Bismark completed in 0d 0h 38m 9s