Bismark report for: /gscratch/scrubbed/strigg/TRIMG_adapt_5bp/TRIM_cat/CTRL_8C_26psu_2_S18_R1_001_val_1.fq.gz and /gscratch/scrubbed/strigg/TRIMG_adapt_5bp/TRIM_cat/CTRL_8C_26psu_2_S18_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:	33821539
Number of paired-end alignments with a unique best hit:	16988832
Mapping efficiency:	50.2% 
Sequence pairs with no alignments under any condition:	8783250
Sequence pairs did not map uniquely:	8049457
Sequence pairs which were discarded because genomic sequence could not be extracted:	1752

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	4306768	((converted) top strand)
GA/CT/CT:	4163997	(complementary to (converted) top strand)
GA/CT/GA:	4179753	(complementary to (converted) bottom strand)
CT/GA/GA:	4336562	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	618666260

Total methylated C's in CpG context:	53791240
Total methylated C's in CHG context:	2118015
Total methylated C's in CHH context:	13486666
Total methylated C's in Unknown context:	788360


Total unmethylated C's in CpG context:	15384319
Total unmethylated C's in CHG context:	160911871
Total unmethylated C's in CHH context:	372974149
Total unmethylated C's in Unknown context:	1838115


C methylated in CpG context:	77.8%
C methylated in CHG context:	1.3%
C methylated in CHH context:	3.5%
C methylated in unknown context (CN or CHN):	30.0%


Bismark completed in 0d 3h 42m 25s