Bismark report for: /gscratch/scrubbed/strigg/TRIMG_adapt_5bp/TRIM_cat/16C_26psu_4_S16_R1_001_val_1.fq.gz and /gscratch/scrubbed/strigg/TRIMG_adapt_5bp/TRIM_cat/16C_26psu_4_S16_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,-2 -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:	100000
Number of paired-end alignments with a unique best hit:	77872
Mapping efficiency:	77.9% 
Sequence pairs with no alignments under any condition:	190
Sequence pairs did not map uniquely:	21938
Sequence pairs which were discarded because genomic sequence could not be extracted:	12

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	19548	((converted) top strand)
GA/CT/CT:	19138	(complementary to (converted) top strand)
GA/CT/GA:	19291	(complementary to (converted) bottom strand)
CT/GA/GA:	19883	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	3340410

Total methylated C's in CpG context:	219399
Total methylated C's in CHG context:	20697
Total methylated C's in CHH context:	187709
Total methylated C's in Unknown context:	26807


Total unmethylated C's in CpG context:	89115
Total unmethylated C's in CHG context:	762480
Total unmethylated C's in CHH context:	2061010
Total unmethylated C's in Unknown context:	79066


C methylated in CpG context:	71.1%
C methylated in CHG context:	2.6%
C methylated in CHH context:	8.3%
C methylated in unknown context (CN or CHN):	25.3%


Bismark completed in 0d 0h 2m 46s