Bismark report for: /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-199_S24_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-199_S24_L003_R2_001_val_2.fq.gz (version: v0.21.0)
Bismark was run with Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/lambda/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --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:	100000
Number of paired-end alignments with a unique best hit:	488
Mapping efficiency:	0.5% 
Sequence pairs with no alignments under any condition:	99512
Sequence pairs did not map uniquely:	0
Sequence pairs which were discarded because genomic sequence could not be extracted:	0

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	323	((converted) top strand)
GA/CT/CT:	0	(complementary to (converted) top strand)
GA/CT/GA:	0	(complementary to (converted) bottom strand)
CT/GA/GA:	165	((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:	17466

Total methylated C's in CpG context:	65
Total methylated C's in CHG context:	190
Total methylated C's in CHH context:	74
Total methylated C's in Unknown context:	4

Total unmethylated C's in CpG context:	4904
Total unmethylated C's in CHG context:	4687
Total unmethylated C's in CHH context:	7546
Total unmethylated C's in Unknown context:	5

C methylated in CpG context:	1.3%
C methylated in CHG context:	3.9%
C methylated in CHH context:	1.0%
C methylated in unknown context (CN or CHN):	44.4%


Bismark completed in 0d 0h 0m 10s