Bismark report for: /gscratch/scrubbed/strigg/TRIMG_adapt_5bp/TRIM_cat/Sealice_F1_S20_R1_001_val_1.fq.gz and /gscratch/scrubbed/strigg/TRIMG_adapt_5bp/TRIM_cat/Sealice_F1_S20_R2_001_val_2.fq.gz (version: v0.19.0)
Bismark was run with Bowtie 2 against the bisulfite genome of /gscratch/srlab/strigg/data/Caligus/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:	225746922
Number of paired-end alignments with a unique best hit:	63327611
Mapping efficiency:	28.1% 
Sequence pairs with no alignments under any condition:	121134921
Sequence pairs did not map uniquely:	41284390
Sequence pairs which were discarded because genomic sequence could not be extracted:	3

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	17963269	((converted) top strand)
GA/CT/CT:	13634042	(complementary to (converted) top strand)
GA/CT/GA:	13707963	(complementary to (converted) bottom strand)
CT/GA/GA:	18022334	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	2717362145

Total methylated C's in CpG context:	5831950
Total methylated C's in CHG context:	5234399
Total methylated C's in CHH context:	28580018
Total methylated C's in Unknown context:	3139344


Total unmethylated C's in CpG context:	414300782
Total unmethylated C's in CHG context:	433425327
Total unmethylated C's in CHH context:	1829989669
Total unmethylated C's in Unknown context:	24817838


C methylated in CpG context:	1.4%
C methylated in CHG context:	1.2%
C methylated in CHH context:	1.5%
C methylated in unknown context (CN or CHN):	11.2%


Bismark completed in 0d 17h 9m 40s