Bismark report for: /gscratch/scrubbed/strigg/TRIMG_adapt_5bp/TRIM_cat/CTRL_16C_26psu_1_S19_R1_001_val_1.fq.gz and /gscratch/scrubbed/strigg/TRIMG_adapt_5bp/TRIM_cat/CTRL_16C_26psu_1_S19_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,-1 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --minins 60 --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:	100000
Number of paired-end alignments with a unique best hit:	56796
Mapping efficiency:	56.8% 
Sequence pairs with no alignments under any condition:	25589
Sequence pairs did not map uniquely:	17615
Sequence pairs which were discarded because genomic sequence could not be extracted:	6

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	14212	((converted) top strand)
GA/CT/CT:	14188	(complementary to (converted) top strand)
GA/CT/GA:	14048	(complementary to (converted) bottom strand)
CT/GA/GA:	14342	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	2556017

Total methylated C's in CpG context:	198106
Total methylated C's in CHG context:	10615
Total methylated C's in CHH context:	57219
Total methylated C's in Unknown context:	7661


Total unmethylated C's in CpG context:	66056
Total unmethylated C's in CHG context:	622136
Total unmethylated C's in CHH context:	1601885
Total unmethylated C's in Unknown context:	27446


C methylated in CpG context:	75.0%
C methylated in CHG context:	1.7%
C methylated in CHH context:	3.4%
C methylated in unknown context (CN or CHN):	21.8%


Bismark completed in 0d 0h 1m 35s