Bismark report for: /gscratch/scrubbed/strigg/Pgen_FQs/EPI-214_S30_L004_R1_001_val_1.fq.gz and /gscratch/scrubbed/strigg/Pgen_FQs/EPI-214_S30_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:	28660043
Number of paired-end alignments with a unique best hit:	13828654
Mapping efficiency:	48.3% 
Sequence pairs with no alignments under any condition:	12337643
Sequence pairs did not map uniquely:	2493746
Sequence pairs which were discarded because genomic sequence could not be extracted:	14

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	6750401	((converted) top strand)
GA/CT/CT:	0	(complementary to (converted) top strand)
GA/CT/GA:	0	(complementary to (converted) bottom strand)
CT/GA/GA:	7078239	((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:	426052941

Total methylated C's in CpG context:	13963490
Total methylated C's in CHG context:	2165482
Total methylated C's in CHH context:	8555313
Total methylated C's in Unknown context:	307555


Total unmethylated C's in CpG context:	46626860
Total unmethylated C's in CHG context:	90587401
Total unmethylated C's in CHH context:	264154395
Total unmethylated C's in Unknown context:	2806908


C methylated in CpG context:	23.0%
C methylated in CHG context:	2.3%
C methylated in CHH context:	3.1%
C methylated in unknown context (CN or CHN):	9.9%


Bismark completed in 0d 2h 16m 13s