Bismark report for: /gscratch/scrubbed/strigg/analyses/20200319/specify_a/EPI-167_S10_L002_R1_001_val_1.fq.gz and /gscratch/scrubbed/strigg/analyses/20200319/specify_a/EPI-167_S10_L002_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:	24340737
Number of paired-end alignments with a unique best hit:	10282831
Mapping efficiency:	42.2% 
Sequence pairs with no alignments under any condition:	11547203
Sequence pairs did not map uniquely:	2510703
Sequence pairs which were discarded because genomic sequence could not be extracted:	7

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	5109279	((converted) top strand)
GA/CT/CT:	0	(complementary to (converted) top strand)
GA/CT/GA:	0	(complementary to (converted) bottom strand)
CT/GA/GA:	5173545	((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:	276968626

Total methylated C's in CpG context:	8922644
Total methylated C's in CHG context:	999800
Total methylated C's in CHH context:	4718477
Total methylated C's in Unknown context:	31009

Total unmethylated C's in CpG context:	25955060
Total unmethylated C's in CHG context:	56364634
Total unmethylated C's in CHH context:	180008011
Total unmethylated C's in Unknown context:	574541

C methylated in CpG context:	25.6%
C methylated in CHG context:	1.7%
C methylated in CHH context:	2.6%
C methylated in unknown context (CN or CHN):	5.1%


Bismark completed in 0d 0h 55m 53s