Bismark report for: /gscratch/srlab/sr320/data/caligus/reads/raw/Sealice_F2_S22_L002_R1_001.fastq.gz and /gscratch/srlab/sr320/data/caligus/reads/raw/Sealice_F2_S22_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:	81699034
Number of paired-end alignments with a unique best hit:	9286200
Mapping efficiency:	11.4% 
Sequence pairs with no alignments under any condition:	67407280
Sequence pairs did not map uniquely:	5005554
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:	2342924	((converted) top strand)
GA/CT/CT:	2317559	(complementary to (converted) top strand)
GA/CT/GA:	2300451	(complementary to (converted) bottom strand)
CT/GA/GA:	2325266	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	520231008

Total methylated C's in CpG context:	2514329
Total methylated C's in CHG context:	1950069
Total methylated C's in CHH context:	8457985
Total methylated C's in Unknown context:	1742408

Total unmethylated C's in CpG context:	82281700
Total unmethylated C's in CHG context:	85424357
Total unmethylated C's in CHH context:	339602568
Total unmethylated C's in Unknown context:	5203451

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 21m 36s