Bismark report for: /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-152_S3_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-152_S3_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/ 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:	29855018
Number of paired-end alignments with a unique best hit:	17480743
Mapping efficiency:	58.6% 
Sequence pairs with no alignments under any condition:	7291555
Sequence pairs did not map uniquely:	5082720
Sequence pairs which were discarded because genomic sequence could not be extracted:	91230

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	7949395	((converted) top strand)
GA/CT/CT:	633023	(complementary to (converted) top strand)
GA/CT/GA:	649555	(complementary to (converted) bottom strand)
CT/GA/GA:	8157540	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	551826884

Total methylated C's in CpG context:	18057953
Total methylated C's in CHG context:	2990393
Total methylated C's in CHH context:	27434841
Total methylated C's in Unknown context:	1000667


Total unmethylated C's in CpG context:	57333026
Total unmethylated C's in CHG context:	111361117
Total unmethylated C's in CHH context:	334649554
Total unmethylated C's in Unknown context:	3107316


C methylated in CpG context:	24.0%
C methylated in CHG context:	2.6%
C methylated in CHH context:	7.6%
C methylated in unknown context (CN or CHN):	24.4%


Bismark completed in 0d 8h 47m 54s