Bismark report for: /gscratch/scrubbed/strigg/TRIMG_adapt_5bp/TRIM_cat/16C_32psu_2_S2_R1_001_val_1.fq.gz and /gscratch/scrubbed/strigg/TRIMG_adapt_5bp/TRIM_cat/16C_32psu_2_S2_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:	35355537
Number of paired-end alignments with a unique best hit:	18964065
Mapping efficiency:	53.6% 
Sequence pairs with no alignments under any condition:	9596391
Sequence pairs did not map uniquely:	6795081
Sequence pairs which were discarded because genomic sequence could not be extracted:	1968

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	5040279	((converted) top strand)
GA/CT/CT:	4389671	(complementary to (converted) top strand)
GA/CT/GA:	4434918	(complementary to (converted) bottom strand)
CT/GA/GA:	5097229	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	770362160

Total methylated C's in CpG context:	56862554
Total methylated C's in CHG context:	2552593
Total methylated C's in CHH context:	14987501
Total methylated C's in Unknown context:	1096199


Total unmethylated C's in CpG context:	18225219
Total unmethylated C's in CHG context:	193626816
Total unmethylated C's in CHH context:	484107477
Total unmethylated C's in Unknown context:	2307573


C methylated in CpG context:	75.7%
C methylated in CHG context:	1.3%
C methylated in CHH context:	3.0%
C methylated in unknown context (CN or CHN):	32.2%


Bismark completed in 0d 4h 10m 45s