Bismark report for: /gscratch/scrubbed/sr320/0924/EPI-161_S8_L002_R1_001_val_1.20bp-trim.fq.gz and /gscratch/scrubbed/sr320/0924/EPI-161_S8_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:	24492789
Number of paired-end alignments with a unique best hit:	8347099
Mapping efficiency:	34.1% 
Sequence pairs with no alignments under any condition:	13726258
Sequence pairs did not map uniquely:	2419432
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:	4106177	((converted) top strand)
GA/CT/CT:	0	(complementary to (converted) top strand)
GA/CT/GA:	0	(complementary to (converted) bottom strand)
CT/GA/GA:	4240922	((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:	193695409

Total methylated C's in CpG context:	6288786
Total methylated C's in CHG context:	569736
Total methylated C's in CHH context:	2419489
Total methylated C's in Unknown context:	28456

Total unmethylated C's in CpG context:	19259401
Total unmethylated C's in CHG context:	39712890
Total unmethylated C's in CHH context:	125445107
Total unmethylated C's in Unknown context:	389018

C methylated in CpG context:	24.6%
C methylated in CHG context:	1.4%
C methylated in CHH context:	1.9%
C methylated in unknown context (CN or CHN):	6.8%


Bismark completed in 0d 1h 17m 30s