Bismark report for: /gscratch/scrubbed/strigg/Pgen_FQs/EPI-215_S31_L004_R1_001_val_1.fq.gz and /gscratch/scrubbed/strigg/Pgen_FQs/EPI-215_S31_L004_R2_001_val_2.fq.gz (version: v0.19.0)
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,-1.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --minins 60 --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:	21150005
Number of paired-end alignments with a unique best hit:	10236960
Mapping efficiency:	48.4% 
Sequence pairs with no alignments under any condition:	8937067
Sequence pairs did not map uniquely:	1975978
Sequence pairs which were discarded because genomic sequence could not be extracted:	24

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	4997699	((converted) top strand)
GA/CT/CT:	0	(complementary to (converted) top strand)
GA/CT/GA:	0	(complementary to (converted) bottom strand)
CT/GA/GA:	5239237	((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:	306752449

Total methylated C's in CpG context:	11752174
Total methylated C's in CHG context:	1777591
Total methylated C's in CHH context:	7279068
Total methylated C's in Unknown context:	275365


Total unmethylated C's in CpG context:	31866501
Total unmethylated C's in CHG context:	65426912
Total unmethylated C's in CHH context:	188650203
Total unmethylated C's in Unknown context:	2057640


C methylated in CpG context:	26.9%
C methylated in CHG context:	2.6%
C methylated in CHH context:	3.7%
C methylated in unknown context (CN or CHN):	11.8%


Bismark completed in 0d 1h 39m 55s