Bismark report for: /gscratch/srlab/strigg/data/Ssalar/FASTQS/20200612/8C_26psu_1_S9_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Ssalar/FASTQS/20200612/8C_26psu_1_S9_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:	35922181
Number of paired-end alignments with a unique best hit:	14030303
Mapping efficiency:	39.1% 
Sequence pairs with no alignments under any condition:	14894341
Sequence pairs did not map uniquely:	6997537
Sequence pairs which were discarded because genomic sequence could not be extracted:	1

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	3541345	((converted) top strand)
GA/CT/CT:	3499850	(complementary to (converted) top strand)
GA/CT/GA:	3476574	(complementary to (converted) bottom strand)
CT/GA/GA:	3512533	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	538202447

Total methylated C's in CpG context:	40951438
Total methylated C's in CHG context:	994353
Total methylated C's in CHH context:	4739798
Total methylated C's in Unknown context:	110622

Total unmethylated C's in CpG context:	11233486
Total unmethylated C's in CHG context:	133217931
Total unmethylated C's in CHH context:	347065441
Total unmethylated C's in Unknown context:	464809

C methylated in CpG context:	78.5%
C methylated in CHG context:	0.7%
C methylated in CHH context:	1.3%
C methylated in unknown context (CN or CHN):	19.2%


Bismark completed in 0d 2h 20m 47s