Bismark report for: /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-135_S35_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-135_S35_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:	28731808
Number of paired-end alignments with a unique best hit:	18358571
Mapping efficiency:	63.9% 
Sequence pairs with no alignments under any condition:	4893497
Sequence pairs did not map uniquely:	5479740
Sequence pairs which were discarded because genomic sequence could not be extracted:	67150

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	8411112	((converted) top strand)
GA/CT/CT:	631208	(complementary to (converted) top strand)
GA/CT/GA:	650614	(complementary to (converted) bottom strand)
CT/GA/GA:	8598487	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	570220880

Total methylated C's in CpG context:	17195669
Total methylated C's in CHG context:	3225591
Total methylated C's in CHH context:	23525793
Total methylated C's in Unknown context:	858420


Total unmethylated C's in CpG context:	63237677
Total unmethylated C's in CHG context:	113217843
Total unmethylated C's in CHH context:	349818307
Total unmethylated C's in Unknown context:	2993331


C methylated in CpG context:	21.4%
C methylated in CHG context:	2.8%
C methylated in CHH context:	6.3%
C methylated in unknown context (CN or CHN):	22.3%


Bismark completed in 0d 8h 52m 46s