Bismark report for: /gscratch/scrubbed/strigg/analyses/20200427/TG_PE_FASTQS/cat_lanes/Sealice_F1_S20_R1_001_val_1.fq.gz and /gscratch/scrubbed/strigg/analyses/20200427/TG_PE_FASTQS/cat_lanes/Sealice_F1_S20_R2_001_val_2.fq.gz (version: v0.22.3)
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:	224907116
Number of paired-end alignments with a unique best hit:	62174415
Mapping efficiency:	27.6% 
Sequence pairs with no alignments under any condition:	112764706
Sequence pairs did not map uniquely:	49967995
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:	17584459	((converted) top strand)
GA/CT/CT:	13556057	(complementary to (converted) top strand)
GA/CT/GA:	13538432	(complementary to (converted) bottom strand)
CT/GA/GA:	17495467	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	2340133640

Total methylated C's in CpG context:	4105081
Total methylated C's in CHG context:	3385525
Total methylated C's in CHH context:	21614155
Total methylated C's in Unknown context:	1617188

Total unmethylated C's in CpG context:	354444893
Total unmethylated C's in CHG context:	366501181
Total unmethylated C's in CHH context:	1590082805
Total unmethylated C's in Unknown context:	21333560

C methylated in CpG context:	1.1%
C methylated in CHG context:	0.9%
C methylated in CHH context:	1.3%
C methylated in unknown context (CN or CHN):	7.0%


Bismark completed in 0d 8h 42m 44s