Bismark report for: /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-169_S12_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-169_S12_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:	41120
Mapping efficiency:	41.1% 
Sequence pairs with no alignments under any condition:	47679
Sequence pairs did not map uniquely:	11201
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:	18966	((converted) top strand)
GA/CT/CT:	1212	(complementary to (converted) top strand)
GA/CT/GA:	1265	(complementary to (converted) bottom strand)
CT/GA/GA:	19677	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	1210712

Total methylated C's in CpG context:	45834
Total methylated C's in CHG context:	6782
Total methylated C's in CHH context:	54452
Total methylated C's in Unknown context:	731

Total unmethylated C's in CpG context:	121772
Total unmethylated C's in CHG context:	247802
Total unmethylated C's in CHH context:	734070
Total unmethylated C's in Unknown context:	2695

C methylated in CpG context:	27.3%
C methylated in CHG context:	2.7%
C methylated in CHH context:	6.9%
C methylated in unknown context (CN or CHN):	21.3%


Bismark completed in 2d 4h 8m 37s