Bismark report for: /gscratch/scrubbed/strigg/TRIMG_adapt_5bp/TRIM_cat/CTRL_16C_26psu_2_S21_R1_001_val_1.fq.gz and /gscratch/scrubbed/strigg/TRIMG_adapt_5bp/TRIM_cat/CTRL_16C_26psu_2_S21_R2_001_val_2.fq.gz (version: v0.19.0)
Bismark was run with Bowtie 2 against the bisulfite genome of /gscratch/srlab/strigg/data/Ssalar/GENOMES/ 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:	26786269
Number of paired-end alignments with a unique best hit:	12679248
Mapping efficiency:	47.3% 
Sequence pairs with no alignments under any condition:	9163307
Sequence pairs did not map uniquely:	4943714
Sequence pairs which were discarded because genomic sequence could not be extracted:	1471

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	3372005	((converted) top strand)
GA/CT/CT:	2929703	(complementary to (converted) top strand)
GA/CT/GA:	2962926	(complementary to (converted) bottom strand)
CT/GA/GA:	3413143	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	505786145

Total methylated C's in CpG context:	44889169
Total methylated C's in CHG context:	2207015
Total methylated C's in CHH context:	8797220
Total methylated C's in Unknown context:	967404


Total unmethylated C's in CpG context:	12901262
Total unmethylated C's in CHG context:	129880538
Total unmethylated C's in CHH context:	307110941
Total unmethylated C's in Unknown context:	2059405


C methylated in CpG context:	77.7%
C methylated in CHG context:	1.7%
C methylated in CHH context:	2.8%
C methylated in unknown context (CN or CHN):	32.0%


Bismark completed in 0d 2h 48m 45s