Bismark report for: /gscratch/scrubbed/strigg/TRIMG_adapt_5bp/TRIM_cat/CTRL_8C_26psu_1_S17_R1_001_val_1.fq.gz and /gscratch/scrubbed/strigg/TRIMG_adapt_5bp/TRIM_cat/CTRL_8C_26psu_1_S17_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,-1.2 -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:	65049
Mapping efficiency:	65.0% 
Sequence pairs with no alignments under any condition:	16751
Sequence pairs did not map uniquely:	18200
Sequence pairs which were discarded because genomic sequence could not be extracted:	13

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	16747	((converted) top strand)
GA/CT/CT:	15782	(complementary to (converted) top strand)
GA/CT/GA:	16127	(complementary to (converted) bottom strand)
CT/GA/GA:	16380	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	2858093

Total methylated C's in CpG context:	187448
Total methylated C's in CHG context:	10595
Total methylated C's in CHH context:	68031
Total methylated C's in Unknown context:	7842


Total unmethylated C's in CpG context:	67624
Total unmethylated C's in CHG context:	660869
Total unmethylated C's in CHH context:	1863526
Total unmethylated C's in Unknown context:	32816


C methylated in CpG context:	73.5%
C methylated in CHG context:	1.6%
C methylated in CHH context:	3.5%
C methylated in unknown context (CN or CHN):	19.3%


Bismark completed in 0d 0h 1m 47s