Bismark report for: /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-194_S23_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-194_S23_L003_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:	27459153
Number of paired-end alignments with a unique best hit:	16621823
Mapping efficiency:	60.5% 
Sequence pairs with no alignments under any condition:	6266029
Sequence pairs did not map uniquely:	4571301
Sequence pairs which were discarded because genomic sequence could not be extracted:	83682

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	8210151	((converted) top strand)
GA/CT/CT:	0	(complementary to (converted) top strand)
GA/CT/GA:	0	(complementary to (converted) bottom strand)
CT/GA/GA:	8327990	((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:	524582345

Total methylated C's in CpG context:	18542819
Total methylated C's in CHG context:	2613561
Total methylated C's in CHH context:	10840662
Total methylated C's in Unknown context:	314640


Total unmethylated C's in CpG context:	56657861
Total unmethylated C's in CHG context:	113333243
Total unmethylated C's in CHH context:	322594199
Total unmethylated C's in Unknown context:	2603525


C methylated in CpG context:	24.7%
C methylated in CHG context:	2.3%
C methylated in CHH context:	3.3%
C methylated in unknown context (CN or CHN):	10.8%


Bismark completed in 0d 6h 18m 24s