Bismark report for: /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-175_S14_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-175_S14_L003_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/v01/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500
Option '--directional' specified (default mode): alignments to complementary strands (CTOT, CTOB) were ignored (i.e. not performed)

Final Alignment report
======================
Sequence pairs analysed in total:	24654280
Number of paired-end alignments with a unique best hit:	10209530
Mapping efficiency:	41.4% 
Sequence pairs with no alignments under any condition:	12327982
Sequence pairs did not map uniquely:	2116768
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:	5041243	((converted) top strand)
GA/CT/CT:	0	(complementary to (converted) top strand)
GA/CT/GA:	0	(complementary to (converted) bottom strand)
CT/GA/GA:	5168286	((converted) bottom strand)

Number of alignments to (merely theoretical) complementary strands being rejected in total:	0

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	309993582

Total methylated C's in CpG context:	11855544
Total methylated C's in CHG context:	1437285
Total methylated C's in CHH context:	3685251
Total methylated C's in Unknown context:	57157

Total unmethylated C's in CpG context:	31961048
Total unmethylated C's in CHG context:	65204352
Total unmethylated C's in CHH context:	195850102
Total unmethylated C's in Unknown context:	677780

C methylated in CpG context:	27.1%
C methylated in CHG context:	2.2%
C methylated in CHH context:	1.8%
C methylated in unknown context (CN or CHN):	7.8%


Bismark completed in 0d 1h 24m 42s