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,-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:	163685586
Number of paired-end alignments with a unique best hit:	35458889
Mapping efficiency:	21.7% 
Sequence pairs with no alignments under any condition:	102308578
Sequence pairs did not map uniquely:	25918119
Sequence pairs which were discarded because genomic sequence could not be extracted:	2

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	8957752	((converted) top strand)
GA/CT/CT:	8810464	(complementary to (converted) top strand)
GA/CT/GA:	8783868	(complementary to (converted) bottom strand)
CT/GA/GA:	8906803	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	1537236987

Total methylated C's in CpG context:	3260062
Total methylated C's in CHG context:	2642635
Total methylated C's in CHH context:	16005844
Total methylated C's in Unknown context:	1753344


Total unmethylated C's in CpG context:	247403724
Total unmethylated C's in CHG context:	256800799
Total unmethylated C's in CHH context:	1011123923
Total unmethylated C's in Unknown context:	13508493


C methylated in CpG context:	1.3%
C methylated in CHG context:	1.0%
C methylated in CHH context:	1.6%
C methylated in unknown context (CN or CHN):	11.5%


Bismark completed in 0d 10h 50m 20s