Bismark report for: /gscratch/srlab/sr320/data/caligus/reads/raw/Sealice_F1_S20_L001_R1_001.fastq.gz and /gscratch/srlab/sr320/data/caligus/reads/raw/Sealice_F1_S20_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:	113474961
Number of paired-end alignments with a unique best hit:	18071283
Mapping efficiency:	15.9% 
Sequence pairs with no alignments under any condition:	86568022
Sequence pairs did not map uniquely:	8835656
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:	5072942	((converted) top strand)
GA/CT/CT:	3933628	(complementary to (converted) top strand)
GA/CT/GA:	3960012	(complementary to (converted) bottom strand)
CT/GA/GA:	5104700	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	979199135

Total methylated C's in CpG context:	4118192
Total methylated C's in CHG context:	3393802
Total methylated C's in CHH context:	15178693
Total methylated C's in Unknown context:	2887891

Total unmethylated C's in CpG context:	146098875
Total unmethylated C's in CHG context:	153307574
Total unmethylated C's in CHH context:	657101999
Total unmethylated C's in Unknown context:	10034093

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):	22.3%


Bismark completed in 0d 6h 54m 58s