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 '--non_directional' specified: alignments to all strands were being performed (OT, OB, CTOT, CTOB)

Final Alignment report
======================
Sequence pairs analysed in total:	112706276
Number of paired-end alignments with a unique best hit:	17528111
Mapping efficiency:	15.6% 
Sequence pairs with no alignments under any condition:	86586560
Sequence pairs did not map uniquely:	8591605
Sequence pairs which were discarded because genomic sequence could not be extracted:	1

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	4922482	((converted) top strand)
GA/CT/CT:	3813994	(complementary to (converted) top strand)
GA/CT/GA:	3840498	(complementary to (converted) bottom strand)
CT/GA/GA:	4951136	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	949354763

Total methylated C's in CpG context:	3989154
Total methylated C's in CHG context:	3288380
Total methylated C's in CHH context:	14679832
Total methylated C's in Unknown context:	2785517

Total unmethylated C's in CpG context:	141676841
Total unmethylated C's in CHG context:	148657726
Total unmethylated C's in CHH context:	637062830
Total unmethylated C's in Unknown context:	9671815

C methylated in CpG context:	2.7%
C methylated in CHG context:	2.2%
C methylated in CHH context:	2.3%
C methylated in unknown context (CN or CHN):	22.4%


Bismark completed in 0d 6h 50m 20s