Bismark report for: ../data/raw-wgbs/239M_1.fastq.gz and ../data/raw-wgbs/239M_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:	108112211
Number of paired-end alignments with a unique best hit:	50719282
Mapping efficiency:	46.9% 
Sequence pairs with no alignments under any condition:	44684722
Sequence pairs did not map uniquely:	12708207
Sequence pairs which were discarded because genomic sequence could not be extracted:	71

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	25371954	((converted) top strand)
GA/CT/CT:	5556	(complementary to (converted) top strand)
GA/CT/GA:	5051	(complementary to (converted) bottom strand)
CT/GA/GA:	25336650	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	2378079434

Total methylated C's in CpG context:	39483148
Total methylated C's in CHG context:	11296787
Total methylated C's in CHH context:	55941539
Total methylated C's in Unknown context:	3115796

Total unmethylated C's in CpG context:	232242348
Total unmethylated C's in CHG context:	368776059
Total unmethylated C's in CHH context:	1670339553
Total unmethylated C's in Unknown context:	10902559

C methylated in CpG context:	14.5%
C methylated in CHG context:	3.0%
C methylated in CHH context:	3.2%
C methylated in Unknown context (CN or CHN):	22.2%


Bismark completed in 0d 6h 15m 44s