Bismark report for: /gscratch/srlab/sr320/data/caligus/reads/raw/Sealice_F2_S22_L001_R1_001.fastq.gz and /gscratch/srlab/sr320/data/caligus/reads/raw/Sealice_F2_S22_L001_R2_001.fastq.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:	82177525
Number of paired-end alignments with a unique best hit:	9562005
Mapping efficiency:	11.6% 
Sequence pairs with no alignments under any condition:	67475294
Sequence pairs did not map uniquely:	5140226
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:	2412884	((converted) top strand)
GA/CT/CT:	2384062	(complementary to (converted) top strand)
GA/CT/GA:	2370078	(complementary to (converted) bottom strand)
CT/GA/GA:	2394981	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	535876331

Total methylated C's in CpG context:	2593525
Total methylated C's in CHG context:	2007967
Total methylated C's in CHH context:	8733191
Total methylated C's in Unknown context:	1806572

Total unmethylated C's in CpG context:	84745811
Total unmethylated C's in CHG context:	87968326
Total unmethylated C's in CHH context:	349827511
Total unmethylated C's in Unknown context:	5392599

C methylated in CpG context:	3.0%
C methylated in CHG context:	2.2%
C methylated in CHH context:	2.4%
C methylated in unknown context (CN or CHN):	25.1%


Bismark completed in 0d 4h 24m 58s