Bismark report for: /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-184_S18_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-184_S18_L003_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:	42466
Mapping efficiency:	42.5% 
Sequence pairs with no alignments under any condition:	47104
Sequence pairs did not map uniquely:	10430
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:	20028	((converted) top strand)
GA/CT/CT:	1077	(complementary to (converted) top strand)
GA/CT/GA:	1094	(complementary to (converted) bottom strand)
CT/GA/GA:	20267	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	1283864

Total methylated C's in CpG context:	48464
Total methylated C's in CHG context:	6495
Total methylated C's in CHH context:	46806
Total methylated C's in Unknown context:	595

Total unmethylated C's in CpG context:	126521
Total unmethylated C's in CHG context:	264415
Total unmethylated C's in CHH context:	791163
Total unmethylated C's in Unknown context:	2996

C methylated in CpG context:	27.7%
C methylated in CHG context:	2.4%
C methylated in CHH context:	5.6%
C methylated in unknown context (CN or CHN):	16.6%


Bismark completed in 2d 17h 6m 34s