Bismark report for: /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-111_S29_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-111_S29_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:	10000
Number of paired-end alignments with a unique best hit:	6440
Mapping efficiency:	64.4% 
Sequence pairs with no alignments under any condition:	1698
Sequence pairs did not map uniquely:	1862
Sequence pairs which were discarded because genomic sequence could not be extracted:	27

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	3050	((converted) top strand)
GA/CT/CT:	176	(complementary to (converted) top strand)
GA/CT/GA:	172	(complementary to (converted) bottom strand)
CT/GA/GA:	3015	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	200670

Total methylated C's in CpG context:	5920
Total methylated C's in CHG context:	989
Total methylated C's in CHH context:	6386
Total methylated C's in Unknown context:	270


Total unmethylated C's in CpG context:	21438
Total unmethylated C's in CHG context:	40265
Total unmethylated C's in CHH context:	125672
Total unmethylated C's in Unknown context:	1005


C methylated in CpG context:	21.6%
C methylated in CHG context:	2.4%
C methylated in CHH context:	4.8%
C methylated in unknown context (CN or CHN):	21.2%


Bismark completed in 0d 0h 0m 55s