Bismark report for: /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-227_S35_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-227_S35_L004_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 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --minins 60 --maxins 500
Option '--directional' specified (default mode): alignments to complementary strands (CTOT, CTOB) were ignored (i.e. not performed)

Final Alignment report
======================
Sequence pairs analysed in total:	13531234
Number of paired-end alignments with a unique best hit:	7734248
Mapping efficiency:	57.2% 
Sequence pairs with no alignments under any condition:	3471625
Sequence pairs did not map uniquely:	2325361
Sequence pairs which were discarded because genomic sequence could not be extracted:	29630

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	3835808	((converted) top strand)
GA/CT/CT:	0	(complementary to (converted) top strand)
GA/CT/GA:	0	(complementary to (converted) bottom strand)
CT/GA/GA:	3868810	((converted) bottom strand)

Number of alignments to (merely theoretical) complementary strands being rejected in total:	0

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	239457122

Total methylated C's in CpG context:	8334082
Total methylated C's in CHG context:	1391647
Total methylated C's in CHH context:	9119902
Total methylated C's in Unknown context:	277190


Total unmethylated C's in CpG context:	25290325
Total unmethylated C's in CHG context:	50181960
Total unmethylated C's in CHH context:	145139206
Total unmethylated C's in Unknown context:	1149172


C methylated in CpG context:	24.8%
C methylated in CHG context:	2.7%
C methylated in CHH context:	5.9%
C methylated in unknown context (CN or CHN):	19.4%


Bismark completed in 0d 2h 53m 32s