Bismark report for: /gscratch/scrubbed/strigg/TRIMG_adapt_5bp/TRIM_cat/16C_26psu_2_S14_R1_001_val_1.fq.gz and /gscratch/scrubbed/strigg/TRIMG_adapt_5bp/TRIM_cat/16C_26psu_2_S14_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,-0.2 -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:	33792
Mapping efficiency:	33.8% 
Sequence pairs with no alignments under any condition:	52674
Sequence pairs did not map uniquely:	13534
Sequence pairs which were discarded because genomic sequence could not be extracted:	2

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	8605	((converted) top strand)
GA/CT/CT:	8267	(complementary to (converted) top strand)
GA/CT/GA:	8295	(complementary to (converted) bottom strand)
CT/GA/GA:	8623	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	1489578

Total methylated C's in CpG context:	114640
Total methylated C's in CHG context:	2845
Total methylated C's in CHH context:	13439
Total methylated C's in Unknown context:	301


Total unmethylated C's in CpG context:	31821
Total unmethylated C's in CHG context:	372830
Total unmethylated C's in CHH context:	954003
Total unmethylated C's in Unknown context:	813


C methylated in CpG context:	78.3%
C methylated in CHG context:	0.8%
C methylated in CHH context:	1.4%
C methylated in unknown context (CN or CHN):	27.0%


Bismark completed in 0d 0h 1m 20s