Bismark report for: /gscratch/scrubbed/strigg/TRIMG_adapt_5bp/TRIM_cat/16C_26psu_1_S13_R1_001_val_1.fq.gz and /gscratch/scrubbed/strigg/TRIMG_adapt_5bp/TRIM_cat/16C_26psu_1_S13_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:	78584
Mapping efficiency:	78.6% 
Sequence pairs with no alignments under any condition:	187
Sequence pairs did not map uniquely:	21229
Sequence pairs which were discarded because genomic sequence could not be extracted:	24

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	20369	((converted) top strand)
GA/CT/CT:	18825	(complementary to (converted) top strand)
GA/CT/GA:	18876	(complementary to (converted) bottom strand)
CT/GA/GA:	20490	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	3482248

Total methylated C's in CpG context:	231653
Total methylated C's in CHG context:	21546
Total methylated C's in CHH context:	165629
Total methylated C's in Unknown context:	27435


Total unmethylated C's in CpG context:	99009
Total unmethylated C's in CHG context:	794288
Total unmethylated C's in CHH context:	2170123
Total unmethylated C's in Unknown context:	85883


C methylated in CpG context:	70.1%
C methylated in CHG context:	2.6%
C methylated in CHH context:	7.1%
C methylated in unknown context (CN or CHN):	24.2%


Bismark completed in 0d 0h 2m 47s