Bismark report for: /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-42_S39_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-42_S39_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:	6178
Mapping efficiency:	61.8% 
Sequence pairs with no alignments under any condition:	1925
Sequence pairs did not map uniquely:	1897
Sequence pairs which were discarded because genomic sequence could not be extracted:	29

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	2758	((converted) top strand)
GA/CT/CT:	350	(complementary to (converted) top strand)
GA/CT/GA:	316	(complementary to (converted) bottom strand)
CT/GA/GA:	2725	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	181548

Total methylated C's in CpG context:	6365
Total methylated C's in CHG context:	1121
Total methylated C's in CHH context:	11440
Total methylated C's in Unknown context:	442


Total unmethylated C's in CpG context:	17527
Total unmethylated C's in CHG context:	36119
Total unmethylated C's in CHH context:	108976
Total unmethylated C's in Unknown context:	1009


C methylated in CpG context:	26.6%
C methylated in CHG context:	3.0%
C methylated in CHH context:	9.5%
C methylated in unknown context (CN or CHN):	30.5%


Bismark completed in 0d 0h 0m 56s