Bismark report for: /gscratch/srlab/strigg/data/Ssalar/FASTQS/20200612/16C_32psu_1_S1_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Ssalar/FASTQS/20200612/16C_32psu_1_S1_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:	38673596
Number of paired-end alignments with a unique best hit:	15311275
Mapping efficiency:	39.6% 
Sequence pairs with no alignments under any condition:	14493212
Sequence pairs did not map uniquely:	8869109
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:	4009554	((converted) top strand)
GA/CT/CT:	3662413	(complementary to (converted) top strand)
GA/CT/GA:	3643974	(complementary to (converted) bottom strand)
CT/GA/GA:	3995334	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	546305422

Total methylated C's in CpG context:	43358893
Total methylated C's in CHG context:	929219
Total methylated C's in CHH context:	4602687
Total methylated C's in Unknown context:	112116

Total unmethylated C's in CpG context:	11980444
Total unmethylated C's in CHG context:	135090410
Total unmethylated C's in CHH context:	350343769
Total unmethylated C's in Unknown context:	445997

C methylated in CpG context:	78.4%
C methylated in CHG context:	0.7%
C methylated in CHH context:	1.3%
C methylated in unknown context (CN or CHN):	20.1%


Bismark completed in 0d 2h 26m 52s