Bismark report for: ../../data/raw-wgbs/106M_1.fastq.gz and ../../data/raw-wgbs/106M_2.fastq.gz (version: v0.24.2)
Bismark was run with Bowtie 2 against the bisulfite genome of /mmfs1/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:	10000
Number of paired-end alignments with a unique best hit:	4749
Mapping efficiency:	47.5% 
Sequence pairs with no alignments under any condition:	4085
Sequence pairs did not map uniquely:	1166
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:	2375	((converted) top strand)
GA/CT/CT:	1	(complementary to (converted) top strand)
GA/CT/GA:	0	(complementary to (converted) bottom strand)
CT/GA/GA:	2373	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	223389

Total methylated C's in CpG context:	3541
Total methylated C's in CHG context:	978
Total methylated C's in CHH context:	4969
Total methylated C's in Unknown context:	256

Total unmethylated C's in CpG context:	22163
Total unmethylated C's in CHG context:	34962
Total unmethylated C's in CHH context:	156776
Total unmethylated C's in Unknown context:	1048

C methylated in CpG context:	13.8%
C methylated in CHG context:	2.7%
C methylated in CHH context:	3.1%
C methylated in Unknown context (CN or CHN):	19.6%


Bismark completed in 0d 0h 0m 27s