Bismark report for: /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-154_S5_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-154_S5_L002_R2_001_val_2.fq.gz (version: v0.21.0_dev)
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 28 --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:	100000
Number of paired-end alignments with a unique best hit:	38638
Mapping efficiency:	38.6% 
Sequence pairs with no alignments under any condition:	52838
Sequence pairs did not map uniquely:	8524
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:	18164	((converted) top strand)
GA/CT/CT:	886	(complementary to (converted) top strand)
GA/CT/GA:	865	(complementary to (converted) bottom strand)
CT/GA/GA:	18723	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	1187602

Total methylated C's in CpG context:	45245
Total methylated C's in CHG context:	5749
Total methylated C's in CHH context:	46056
Total methylated C's in Unknown context:	597

Total unmethylated C's in CpG context:	113591
Total unmethylated C's in CHG context:	240273
Total unmethylated C's in CHH context:	736688
Total unmethylated C's in Unknown context:	2664

C methylated in CpG context:	28.5%
C methylated in CHG context:	2.3%
C methylated in CHH context:	5.9%
C methylated in unknown context (CN or CHN):	18.3%


Bismark completed in 1d 13h 5m 43s