Bismark report for: /gscratch/scrubbed/strigg/TRIMG_adapt_5bp/TRIM_cat/Sealice_F2_S22_R1_001_val_1.fq.gz and /gscratch/scrubbed/strigg/TRIMG_adapt_5bp/TRIM_cat/Sealice_F2_S22_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,-1 -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:	30940
Mapping efficiency:	30.9% 
Sequence pairs with no alignments under any condition:	50376
Sequence pairs did not map uniquely:	18684
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:	7782	((converted) top strand)
GA/CT/CT:	7756	(complementary to (converted) top strand)
GA/CT/GA:	7794	(complementary to (converted) bottom strand)
CT/GA/GA:	7608	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	1312308

Total methylated C's in CpG context:	3420
Total methylated C's in CHG context:	2928
Total methylated C's in CHH context:	20096
Total methylated C's in Unknown context:	2818


Total unmethylated C's in CpG context:	211145
Total unmethylated C's in CHG context:	215783
Total unmethylated C's in CHH context:	858936
Total unmethylated C's in Unknown context:	20903


C methylated in CpG context:	1.6%
C methylated in CHG context:	1.3%
C methylated in CHH context:	2.3%
C methylated in unknown context (CN or CHN):	11.9%


Bismark completed in 0d 0h 0m 44s