Bismark report for: ../data/raw-wgbs/105M_1.fastq.gz and ../data/raw-wgbs/105M_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:	92976446
Number of paired-end alignments with a unique best hit:	43928243
Mapping efficiency:	47.2% 
Sequence pairs with no alignments under any condition:	37402868
Sequence pairs did not map uniquely:	11645335
Sequence pairs which were discarded because genomic sequence could not be extracted:	77

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	21990891	((converted) top strand)
GA/CT/CT:	6461	(complementary to (converted) top strand)
GA/CT/GA:	6205	(complementary to (converted) bottom strand)
CT/GA/GA:	21924609	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	2085981248

Total methylated C's in CpG context:	31378944
Total methylated C's in CHG context:	9663023
Total methylated C's in CHH context:	48051307
Total methylated C's in Unknown context:	2340545

Total unmethylated C's in CpG context:	212943760
Total unmethylated C's in CHG context:	326653235
Total unmethylated C's in CHH context:	1457290979
Total unmethylated C's in Unknown context:	8800113

C methylated in CpG context:	12.8%
C methylated in CHG context:	2.9%
C methylated in CHH context:	3.2%
C methylated in Unknown context (CN or CHN):	21.0%


Bismark completed in 0d 5h 19m 27s