Bismark report for: /gscratch/srlab/sr320/data/caligus/Sealice_F1_S20_L001_R1_001_val_1_val_1.fq.gz and /gscratch/srlab/sr320/data/caligus/Sealice_F1_S20_L001_R2_001_val_2_val_2.fq.gz (version: v0.21.0)
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,-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:	112799336
Number of paired-end alignments with a unique best hit:	532093
Mapping efficiency:	0.5% 
Sequence pairs with no alignments under any condition:	112048372
Sequence pairs did not map uniquely:	218871
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:	270168	((converted) top strand)
GA/CT/CT:	0	(complementary to (converted) top strand)
GA/CT/GA:	0	(complementary to (converted) bottom strand)
CT/GA/GA:	261925	((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:	6792462

Total methylated C's in CpG context:	44803
Total methylated C's in CHG context:	37016
Total methylated C's in CHH context:	2099417
Total methylated C's in Unknown context:	32004

Total unmethylated C's in CpG context:	376529
Total unmethylated C's in CHG context:	446628
Total unmethylated C's in CHH context:	3788069
Total unmethylated C's in Unknown context:	47091

C methylated in CpG context:	10.6%
C methylated in CHG context:	7.7%
C methylated in CHH context:	35.7%
C methylated in unknown context (CN or CHN):	40.5%


Bismark completed in 0d 3h 39m 20s