Bismark report for: /gscratch/srlab/strigg/data/Pgenr/FASTQS/data_for_genome_comparison/EPI-119_S31_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/data_for_genome_comparison/EPI-119_S31_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/Pgenr_070_10K/ 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:	28905983
Number of paired-end alignments with a unique best hit:	16962818
Mapping efficiency:	58.7% 
Sequence pairs with no alignments under any condition:	7651911
Sequence pairs did not map uniquely:	4291254
Sequence pairs which were discarded because genomic sequence could not be extracted:	33998

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	8601516	((converted) top strand)
GA/CT/CT:	0	(complementary to (converted) top strand)
GA/CT/GA:	0	(complementary to (converted) bottom strand)
CT/GA/GA:	8327304	((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:	544456988

Total methylated C's in CpG context:	15192805
Total methylated C's in CHG context:	2451365
Total methylated C's in CHH context:	5312411
Total methylated C's in Unknown context:	165184


Total unmethylated C's in CpG context:	65321692
Total unmethylated C's in CHG context:	113561366
Total unmethylated C's in CHH context:	342617349
Total unmethylated C's in Unknown context:	2927480


C methylated in CpG context:	18.9%
C methylated in CHG context:	2.1%
C methylated in CHH context:	1.5%
C methylated in unknown context (CN or CHN):	5.3%


Bismark completed in 0d 6h 47m 56s