Bismark report for: /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-119_S31_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-119_S31_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:	28905983
Number of paired-end alignments with a unique best hit:	18510081
Mapping efficiency:	64.0% 
Sequence pairs with no alignments under any condition:	5236342
Sequence pairs did not map uniquely:	5159560
Sequence pairs which were discarded because genomic sequence could not be extracted:	55302

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	8628401	((converted) top strand)
GA/CT/CT:	445598	(complementary to (converted) top strand)
GA/CT/GA:	455153	(complementary to (converted) bottom strand)
CT/GA/GA:	8925627	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	608728091

Total methylated C's in CpG context:	15666954
Total methylated C's in CHG context:	2916966
Total methylated C's in CHH context:	19314771
Total methylated C's in Unknown context:	692853


Total unmethylated C's in CpG context:	79114881
Total unmethylated C's in CHG context:	122174524
Total unmethylated C's in CHH context:	369539995
Total unmethylated C's in Unknown context:	3002445


C methylated in CpG context:	16.5%
C methylated in CHG context:	2.3%
C methylated in CHH context:	5.0%
C methylated in unknown context (CN or CHN):	18.7%


Bismark completed in 0d 8h 38m 19s