Bismark report for: /gscratch/srlab/sr320/data/caligus/reads/raw/Sealice_F1_S20_L002_R1_001.fastq.gz and /gscratch/srlab/sr320/data/caligus/reads/raw/Sealice_F1_S20_L002_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 '--directional' specified (default mode): alignments to complementary strands (CTOT, CTOB) were ignored (i.e. not performed)

Final Alignment report
======================
Sequence pairs analysed in total:	112706276
Number of paired-end alignments with a unique best hit:	9883349
Mapping efficiency:	8.8% 
Sequence pairs with no alignments under any condition:	98036031
Sequence pairs did not map uniquely:	4786896
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:	4927716	((converted) top strand)
GA/CT/CT:	0	(complementary to (converted) top strand)
GA/CT/GA:	0	(complementary to (converted) bottom strand)
CT/GA/GA:	4955633	((converted) bottom strand)

Number of alignments to (merely theoretical) complementary strands being rejected in total:	0

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	534355619

Total methylated C's in CpG context:	2419146
Total methylated C's in CHG context:	1992060
Total methylated C's in CHH context:	9421424
Total methylated C's in Unknown context:	1713666

Total unmethylated C's in CpG context:	79153095
Total unmethylated C's in CHG context:	83267009
Total unmethylated C's in CHH context:	358102885
Total unmethylated C's in Unknown context:	5385442

C methylated in CpG context:	3.0%
C methylated in CHG context:	2.3%
C methylated in CHH context:	2.6%
C methylated in unknown context (CN or CHN):	24.1%


Bismark completed in 0d 6h 30m 34s