Bismark report for: /gscratch/scrubbed/sr320/0924/EPI-162_S9_L002_R1_001_val_1.20bp-trim.fq.gz and /gscratch/scrubbed/sr320/0924/EPI-162_S9_L002_R2_001_val_2.20bp-trim.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:	22746423
Number of paired-end alignments with a unique best hit:	7982139
Mapping efficiency:	35.1% 
Sequence pairs with no alignments under any condition:	12293756
Sequence pairs did not map uniquely:	2470528
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:	3917194	((converted) top strand)
GA/CT/CT:	0	(complementary to (converted) top strand)
GA/CT/GA:	0	(complementary to (converted) bottom strand)
CT/GA/GA:	4064945	((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:	182398480

Total methylated C's in CpG context:	5917870
Total methylated C's in CHG context:	561612
Total methylated C's in CHH context:	2425318
Total methylated C's in Unknown context:	26840

Total unmethylated C's in CpG context:	18231986
Total unmethylated C's in CHG context:	37832540
Total unmethylated C's in CHH context:	117429154
Total unmethylated C's in Unknown context:	378028

C methylated in CpG context:	24.5%
C methylated in CHG context:	1.5%
C methylated in CHH context:	2.0%
C methylated in unknown context (CN or CHN):	6.6%


Bismark completed in 0d 1h 15m 19s