Bismark report for: /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-206_S27_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-206_S27_L004_R2_001_val_2.fq.gz (version: v0.21.0_dev)
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 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500
Option '--non_directional' specified: alignments to all strands were being performed (OT, OB, CTOT, CTOB)

Final Alignment report
======================
Sequence pairs analysed in total:	100000
Number of paired-end alignments with a unique best hit:	43502
Mapping efficiency:	43.5% 
Sequence pairs with no alignments under any condition:	43133
Sequence pairs did not map uniquely:	13365
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:	20106	((converted) top strand)
GA/CT/CT:	1437	(complementary to (converted) top strand)
GA/CT/GA:	1424	(complementary to (converted) bottom strand)
CT/GA/GA:	20535	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	1251141

Total methylated C's in CpG context:	50142
Total methylated C's in CHG context:	7138
Total methylated C's in CHH context:	52714
Total methylated C's in Unknown context:	752

Total unmethylated C's in CpG context:	127409
Total unmethylated C's in CHG context:	259611
Total unmethylated C's in CHH context:	754127
Total unmethylated C's in Unknown context:	2750

C methylated in CpG context:	28.2%
C methylated in CHG context:	2.7%
C methylated in CHH context:	6.5%
C methylated in unknown context (CN or CHN):	21.5%


Bismark completed in 3d 12h 27m 56s