Bismark report for: ../data/raw-wgbs/242M_1.fastq.gz and ../data/raw-wgbs/242M_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:	86793768
Number of paired-end alignments with a unique best hit:	40866671
Mapping efficiency:	47.1% 
Sequence pairs with no alignments under any condition:	31531236
Sequence pairs did not map uniquely:	14395861
Sequence pairs which were discarded because genomic sequence could not be extracted:	102

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	20472681	((converted) top strand)
GA/CT/CT:	8285	(complementary to (converted) top strand)
GA/CT/GA:	7939	(complementary to (converted) bottom strand)
CT/GA/GA:	20377664	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	2099732888

Total methylated C's in CpG context:	39803056
Total methylated C's in CHG context:	10013472
Total methylated C's in CHH context:	48291258
Total methylated C's in Unknown context:	2784447

Total unmethylated C's in CpG context:	240672757
Total unmethylated C's in CHG context:	345973129
Total unmethylated C's in CHH context:	1414979216
Total unmethylated C's in Unknown context:	9128068

C methylated in CpG context:	14.2%
C methylated in CHG context:	2.8%
C methylated in CHH context:	3.3%
C methylated in Unknown context (CN or CHN):	23.4%


Bismark completed in 0d 5h 40m 1s