Bismark report for: /gscratch/srlab/strigg/data/Ssalar/FASTQS/20200612/CTRL_16C_26psu_1_S19_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Ssalar/FASTQS/20200612/CTRL_16C_26psu_1_S19_R2_001_val_2.fq.gz (version: v0.22.3)
Bismark was run with Bowtie 2 against the bisulfite genome of /gscratch/srlab/strigg/data/Ssalar/GENOMES/2022/ with the specified options: -q --score-min L,0,-0.3 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --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:	36791002
Number of paired-end alignments with a unique best hit:	13577162
Mapping efficiency:	36.9% 
Sequence pairs with no alignments under any condition:	16161364
Sequence pairs did not map uniquely:	7052476
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:	3443155	((converted) top strand)
GA/CT/CT:	3366463	(complementary to (converted) top strand)
GA/CT/GA:	3344003	(complementary to (converted) bottom strand)
CT/GA/GA:	3423541	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	517388379

Total methylated C's in CpG context:	41891312
Total methylated C's in CHG context:	898456
Total methylated C's in CHH context:	3971510
Total methylated C's in Unknown context:	118558

Total unmethylated C's in CpG context:	11224741
Total unmethylated C's in CHG context:	127076016
Total unmethylated C's in CHH context:	332326344
Total unmethylated C's in Unknown context:	466756

C methylated in CpG context:	78.9%
C methylated in CHG context:	0.7%
C methylated in CHH context:	1.2%
C methylated in unknown context (CN or CHN):	20.3%


Bismark completed in 0d 2h 15m 58s