Bismark report for: /gscratch/scrubbed/sr320/pg_all/Pg_val_1.fq.gz and /gscratch/scrubbed/sr320/pg_all/Pg_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:	1237279577
Number of paired-end alignments with a unique best hit:	510447476
Mapping efficiency:	41.3% 
Sequence pairs with no alignments under any condition:	612597329
Sequence pairs did not map uniquely:	114234772
Sequence pairs which were discarded because genomic sequence could not be extracted:	86

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	252090696	((converted) top strand)
GA/CT/CT:	0	(complementary to (converted) top strand)
GA/CT/GA:	0	(complementary to (converted) bottom strand)
CT/GA/GA:	258356694	((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:	15255999761

Total methylated C's in CpG context:	591642424
Total methylated C's in CHG context:	77274827
Total methylated C's in CHH context:	183983876
Total methylated C's in Unknown context:	3101698

Total unmethylated C's in CpG context:	1569847325
Total unmethylated C's in CHG context:	3194099749
Total unmethylated C's in CHH context:	9639151560
Total unmethylated C's in Unknown context:	32722537

C methylated in CpG context:	27.4%
C methylated in CHG context:	2.4%
C methylated in CHH context:	1.9%
C methylated in unknown context (CN or CHN):	8.7%


Bismark completed in 2d 21h 25m 4s