Bismark report for: /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-103_S27_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-103_S27_L005_R2_001_val_2.fq.gz (version: v0.21.0)
Bismark was run with Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v074/ with the specified options: -q --score-min L,0,-0.6 -p 4 --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:	20349659
Number of paired-end alignments with a unique best hit:	9233772
Mapping efficiency:	45.4% 
Sequence pairs with no alignments under any condition:	9350302
Sequence pairs did not map uniquely:	1765585
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:	4473147	((converted) top strand)
GA/CT/CT:	105161	(complementary to (converted) top strand)
GA/CT/GA:	105157	(complementary to (converted) bottom strand)
CT/GA/GA:	4550306	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	297460805

Total methylated C's in CpG context:	9677744
Total methylated C's in CHG context:	1380876
Total methylated C's in CHH context:	7299226
Total methylated C's in Unknown context:	88063

Total unmethylated C's in CpG context:	31148064
Total unmethylated C's in CHG context:	59966133
Total unmethylated C's in CHH context:	187988762
Total unmethylated C's in Unknown context:	637696

C methylated in CpG context:	23.7%
C methylated in CHG context:	2.3%
C methylated in CHH context:	3.7%
C methylated in unknown context (CN or CHN):	12.1%


Bismark completed in 0d 2h 6m 21s