Bismark report for: /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-162_S9_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-162_S9_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:	37601
Mapping efficiency:	37.6% 
Sequence pairs with no alignments under any condition:	51813
Sequence pairs did not map uniquely:	10586
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:	17201	((converted) top strand)
GA/CT/CT:	1235	(complementary to (converted) top strand)
GA/CT/GA:	1150	(complementary to (converted) bottom strand)
CT/GA/GA:	18015	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	1090879

Total methylated C's in CpG context:	38872
Total methylated C's in CHG context:	5795
Total methylated C's in CHH context:	45688
Total methylated C's in Unknown context:	678

Total unmethylated C's in CpG context:	108363
Total unmethylated C's in CHG context:	222063
Total unmethylated C's in CHH context:	670098
Total unmethylated C's in Unknown context:	2505

C methylated in CpG context:	26.4%
C methylated in CHG context:	2.5%
C methylated in CHH context:	6.4%
C methylated in unknown context (CN or CHN):	21.3%


Bismark completed in 1d 21h 20m 44s