Bismark report for: /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-44_S41_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-44_S41_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:	6160
Mapping efficiency:	61.6% 
Sequence pairs with no alignments under any condition:	1937
Sequence pairs did not map uniquely:	1903
Sequence pairs which were discarded because genomic sequence could not be extracted:	24

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	2655	((converted) top strand)
GA/CT/CT:	381	(complementary to (converted) top strand)
GA/CT/GA:	362	(complementary to (converted) bottom strand)
CT/GA/GA:	2738	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	178943

Total methylated C's in CpG context:	6808
Total methylated C's in CHG context:	1030
Total methylated C's in CHH context:	10522
Total methylated C's in Unknown context:	431


Total unmethylated C's in CpG context:	16703
Total unmethylated C's in CHG context:	34940
Total unmethylated C's in CHH context:	108940
Total unmethylated C's in Unknown context:	981


C methylated in CpG context:	29.0%
C methylated in CHG context:	2.9%
C methylated in CHH context:	8.8%
C methylated in unknown context (CN or CHN):	30.5%


Bismark completed in 0d 0h 0m 55s