Bismark report for: /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-151_S2_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-151_S2_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:	24505793
Number of paired-end alignments with a unique best hit:	14968822
Mapping efficiency:	61.1% 
Sequence pairs with no alignments under any condition:	5101533
Sequence pairs did not map uniquely:	4435438
Sequence pairs which were discarded because genomic sequence could not be extracted:	76528

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	6813614	((converted) top strand)
GA/CT/CT:	521544	(complementary to (converted) top strand)
GA/CT/GA:	533992	(complementary to (converted) bottom strand)
CT/GA/GA:	7023144	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	477259696

Total methylated C's in CpG context:	15256198
Total methylated C's in CHG context:	2465327
Total methylated C's in CHH context:	24808682
Total methylated C's in Unknown context:	819054


Total unmethylated C's in CpG context:	53469615
Total unmethylated C's in CHG context:	98506887
Total unmethylated C's in CHH context:	282752987
Total unmethylated C's in Unknown context:	2643085


C methylated in CpG context:	22.2%
C methylated in CHG context:	2.4%
C methylated in CHH context:	8.1%
C methylated in unknown context (CN or CHN):	23.7%


Bismark completed in 0d 7h 8m 55s