Bismark report for: /gscratch/srlab/strigg/data/Ssalar/FASTQS/20200612/8C_32psu_1_S5_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Ssalar/FASTQS/20200612/8C_32psu_1_S5_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:	27432127
Number of paired-end alignments with a unique best hit:	10877689
Mapping efficiency:	39.7% 
Sequence pairs with no alignments under any condition:	8893068
Sequence pairs did not map uniquely:	7661370
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:	2827446	((converted) top strand)
GA/CT/CT:	2630299	(complementary to (converted) top strand)
GA/CT/GA:	2613021	(complementary to (converted) bottom strand)
CT/GA/GA:	2806923	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	349948772

Total methylated C's in CpG context:	30713837
Total methylated C's in CHG context:	612958
Total methylated C's in CHH context:	3206338
Total methylated C's in Unknown context:	70023

Total unmethylated C's in CpG context:	8585777
Total unmethylated C's in CHG context:	90313387
Total unmethylated C's in CHH context:	216516475
Total unmethylated C's in Unknown context:	262623

C methylated in CpG context:	78.2%
C methylated in CHG context:	0.7%
C methylated in CHH context:	1.5%
C methylated in unknown context (CN or CHN):	21.1%


Bismark completed in 0d 1h 39m 55s