Bismark report for: /gscratch/scrubbed/strigg/analyses/20200930/Tank2-025-026_R1_001_val_1.fq.gz and /gscratch/scrubbed/strigg/analyses/20200930/Tank2-025-026_R2_001_val_2.fq.gz (version: v0.22.3)
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 '--non_directional' specified: alignments to all strands were being performed (OT, OB, CTOT, CTOB)

Final Alignment report
======================
Sequence pairs analysed in total:	65947406
Number of paired-end alignments with a unique best hit:	31748771
Mapping efficiency:	48.1% 
Sequence pairs with no alignments under any condition:	30922473
Sequence pairs did not map uniquely:	3276162
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:	15798071	((converted) top strand)
GA/CT/CT:	87134	(complementary to (converted) top strand)
GA/CT/GA:	85413	(complementary to (converted) bottom strand)
CT/GA/GA:	15778146	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	1296491035

Total methylated C's in CpG context:	29427344
Total methylated C's in CHG context:	2816200
Total methylated C's in CHH context:	18823480
Total methylated C's in Unknown context:	170971

Total unmethylated C's in CpG context:	121587680
Total unmethylated C's in CHG context:	223639272
Total unmethylated C's in CHH context:	900197059
Total unmethylated C's in Unknown context:	2947605

C methylated in CpG context:	19.5%
C methylated in CHG context:	1.2%
C methylated in CHH context:	2.0%
C methylated in unknown context (CN or CHN):	5.5%


Bismark completed in 0d 4h 36m 40s