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 /mmfs1/gscratch/scrubbed/sr320/github/project-mytilus-methylation/output/01-bismark-init/ with the specified options: -q --score-min L,0,-0.6 -p 30 --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:	4686
Mapping efficiency:	46.9% 
Sequence pairs with no alignments under any condition:	3640
Sequence pairs did not map uniquely:	1674
Sequence pairs which were discarded because genomic sequence could not be extracted:	1

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	2328	((converted) top strand)
GA/CT/CT:	3	(complementary to (converted) top strand)
GA/CT/GA:	1	(complementary to (converted) bottom strand)
CT/GA/GA:	2353	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	241990

Total methylated C's in CpG context:	4593
Total methylated C's in CHG context:	1148
Total methylated C's in CHH context:	5709
Total methylated C's in Unknown context:	338

Total unmethylated C's in CpG context:	28189
Total unmethylated C's in CHG context:	40000
Total unmethylated C's in CHH context:	162351
Total unmethylated C's in Unknown context:	1056

C methylated in CpG context:	14.0%
C methylated in CHG context:	2.8%
C methylated in CHH context:	3.4%
C methylated in Unknown context (CN or CHN):	24.2%


Bismark completed in 0d 0h 0m 22s