Bismark report for: /gscratch/srlab/sr320/data/caligus/reads/trimmed/sl2/Sealice_F1_S20_L002_R1_001_val_1.fq.gz and /gscratch/srlab/sr320/data/caligus/reads/trimmed/sl2/Sealice_F1_S20_L002_R2_001_val_2.fq.gz (version: v0.21.0)
Bismark was run with Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/caligus/genome/ 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:	112493002
Number of paired-end alignments with a unique best hit:	31358065
Mapping efficiency:	27.9% 
Sequence pairs with no alignments under any condition:	60671476
Sequence pairs did not map uniquely:	20463461
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:	8897914	((converted) top strand)
GA/CT/CT:	6751598	(complementary to (converted) top strand)
GA/CT/GA:	6786829	(complementary to (converted) bottom strand)
CT/GA/GA:	8921722	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	1343425791

Total methylated C's in CpG context:	2886711
Total methylated C's in CHG context:	2595053
Total methylated C's in CHH context:	14140740
Total methylated C's in Unknown context:	1548914

Total unmethylated C's in CpG context:	204897578
Total unmethylated C's in CHG context:	214379403
Total unmethylated C's in CHH context:	904526306
Total unmethylated C's in Unknown context:	12233657

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 6h 51m 14s