Bismark report for: /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-43_S40_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-43_S40_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:	6210
Mapping efficiency:	62.1% 
Sequence pairs with no alignments under any condition:	1863
Sequence pairs did not map uniquely:	1927
Sequence pairs which were discarded because genomic sequence could not be extracted:	22

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	2805	((converted) top strand)
GA/CT/CT:	315	(complementary to (converted) top strand)
GA/CT/GA:	344	(complementary to (converted) bottom strand)
CT/GA/GA:	2724	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	186153

Total methylated C's in CpG context:	6487
Total methylated C's in CHG context:	1015
Total methylated C's in CHH context:	11248
Total methylated C's in Unknown context:	369


Total unmethylated C's in CpG context:	18210
Total unmethylated C's in CHG context:	36502
Total unmethylated C's in CHH context:	112691
Total unmethylated C's in Unknown context:	1069


C methylated in CpG context:	26.3%
C methylated in CHG context:	2.7%
C methylated in CHH context:	9.1%
C methylated in unknown context (CN or CHN):	25.7%


Bismark completed in 0d 0h 0m 54s