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 /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:	88285661
Number of paired-end alignments with a unique best hit:	41908461
Mapping efficiency:	47.5% 
Sequence pairs with no alignments under any condition:	36332293
Sequence pairs did not map uniquely:	10044907
Sequence pairs which were discarded because genomic sequence could not be extracted:	50

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	20973596	((converted) top strand)
GA/CT/CT:	6005	(complementary to (converted) top strand)
GA/CT/GA:	4866	(complementary to (converted) bottom strand)
CT/GA/GA:	20923944	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	1962807409

Total methylated C's in CpG context:	31979766
Total methylated C's in CHG context:	9086543
Total methylated C's in CHH context:	44917378
Total methylated C's in Unknown context:	2178645

Total unmethylated C's in CpG context:	191761640
Total unmethylated C's in CHG context:	305459310
Total unmethylated C's in CHH context:	1379602772
Total unmethylated C's in Unknown context:	8586471

C methylated in CpG context:	14.3%
C methylated in CHG context:	2.9%
C methylated in CHH context:	3.2%
C methylated in Unknown context (CN or CHN):	20.2%


Bismark completed in 0d 4h 49m 35s