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:	100000
Number of paired-end alignments with a unique best hit:	28475
Mapping efficiency:	28.5% 
Sequence pairs with no alignments under any condition:	53180
Sequence pairs did not map uniquely:	18345
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:	8106	((converted) top strand)
GA/CT/CT:	6098	(complementary to (converted) top strand)
GA/CT/GA:	6150	(complementary to (converted) bottom strand)
CT/GA/GA:	8121	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	1218517

Total methylated C's in CpG context:	2632
Total methylated C's in CHG context:	2272
Total methylated C's in CHH context:	12637
Total methylated C's in Unknown context:	1496


Total unmethylated C's in CpG context:	186429
Total unmethylated C's in CHG context:	193960
Total unmethylated C's in CHH context:	820587
Total unmethylated C's in Unknown context:	11129


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):	11.8%


Bismark completed in 0d 0h 0m 43s