Bismark report for: /gscratch/srlab/strigg/data/Salmo_Calig/TRIM_1st5bp/16C_26psu_1_S13_L001_R1_001_trimmed.5bp_3prime.fq.gz and /gscratch/srlab/strigg/data/Salmo_Calig/TRIM_1st5bp/16C_26psu_1_S13_L001_R2_001_trimmed.5bp_3prime.fq.gz (version: v0.19.0)
Bismark was run with Bowtie 2 against the bisulfite genome of /gscratch/srlab/strigg/data/Ssalar/GENOMES/ with the specified options: -q --score-min L,0,-0.6 -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:	100000
Number of paired-end alignments with a unique best hit:	529
Mapping efficiency:	0.5% 
Sequence pairs with no alignments under any condition:	99269
Sequence pairs did not map uniquely:	202
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:	140	((converted) top strand)
GA/CT/CT:	124	(complementary to (converted) top strand)
GA/CT/GA:	126	(complementary to (converted) bottom strand)
CT/GA/GA:	139	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	23240

Total methylated C's in CpG context:	1641
Total methylated C's in CHG context:	92
Total methylated C's in CHH context:	420
Total methylated C's in Unknown context:	30


Total unmethylated C's in CpG context:	621
Total unmethylated C's in CHG context:	5927
Total unmethylated C's in CHH context:	14539
Total unmethylated C's in Unknown context:	85


C methylated in CpG context:	72.5%
C methylated in CHG context:	1.5%
C methylated in CHH context:	2.8%
C methylated in unknown context (CN or CHN):	26.1%


Bismark completed in 0d 0h 1m 16s