Bismark report for: /gscratch/srlab/strigg/data/Ssalar/FASTQS/20200612/16C_32psu_4_S4_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Ssalar/FASTQS/20200612/16C_32psu_4_S4_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:	31149160
Number of paired-end alignments with a unique best hit:	12468000
Mapping efficiency:	40.0% 
Sequence pairs with no alignments under any condition:	13843507
Sequence pairs did not map uniquely:	4837653
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:	3128634	((converted) top strand)
GA/CT/CT:	3122325	(complementary to (converted) top strand)
GA/CT/GA:	3105836	(complementary to (converted) bottom strand)
CT/GA/GA:	3111205	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	513155617

Total methylated C's in CpG context:	36287531
Total methylated C's in CHG context:	829946
Total methylated C's in CHH context:	3691013
Total methylated C's in Unknown context:	103298

Total unmethylated C's in CpG context:	10429257
Total unmethylated C's in CHG context:	121877256
Total unmethylated C's in CHH context:	340040614
Total unmethylated C's in Unknown context:	446750

C methylated in CpG context:	77.7%
C methylated in CHG context:	0.7%
C methylated in CHH context:	1.1%
C methylated in unknown context (CN or CHN):	18.8%


Bismark completed in 0d 1h 59m 58s