Bismark report for: ../data/raw-wgbs/109M_1.fastq.gz and ../data/raw-wgbs/109M_2.fastq.gz (version: v0.24.2)
Bismark was run with Bowtie 2 against the bisulfite genome of /gscratch/scrubbed/sr320/github/project-mytilus-methylation/output/01-bismark-init/ with the specified options: -q --score-min L,0,-0.6 -p 8 --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:	93271100
Number of paired-end alignments with a unique best hit:	44472180
Mapping efficiency:	47.7% 
Sequence pairs with no alignments under any condition:	38219074
Sequence pairs did not map uniquely:	10579846
Sequence pairs which were discarded because genomic sequence could not be extracted:	60

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	22254428	((converted) top strand)
GA/CT/CT:	7234	(complementary to (converted) top strand)
GA/CT/GA:	6628	(complementary to (converted) bottom strand)
CT/GA/GA:	22203830	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	2087963570

Total methylated C's in CpG context:	33633247
Total methylated C's in CHG context:	9624140
Total methylated C's in CHH context:	47818812
Total methylated C's in Unknown context:	2283892

Total unmethylated C's in CpG context:	205848479
Total unmethylated C's in CHG context:	325770817
Total unmethylated C's in CHH context:	1465268075
Total unmethylated C's in Unknown context:	9119364

C methylated in CpG context:	14.0%
C methylated in CHG context:	2.9%
C methylated in CHH context:	3.2%
C methylated in Unknown context (CN or CHN):	20.0%


Bismark completed in 0d 5h 22m 41s