Bismark report for: /gscratch/scrubbed/strigg/TRIMG_adapt_5bp/TRIM_cat/CTRL_16C_26psu_2_S21_R1_001_val_1.fq.gz and /gscratch/scrubbed/strigg/TRIMG_adapt_5bp/TRIM_cat/CTRL_16C_26psu_2_S21_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:	64030
Mapping efficiency:	64.0% 
Sequence pairs with no alignments under any condition:	15716
Sequence pairs did not map uniquely:	20254
Sequence pairs which were discarded because genomic sequence could not be extracted:	11

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	16836	((converted) top strand)
GA/CT/CT:	15073	(complementary to (converted) top strand)
GA/CT/GA:	15159	(complementary to (converted) bottom strand)
CT/GA/GA:	16951	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	2622383

Total methylated C's in CpG context:	221742
Total methylated C's in CHG context:	16087
Total methylated C's in CHH context:	87064
Total methylated C's in Unknown context:	12664


Total unmethylated C's in CpG context:	79024
Total unmethylated C's in CHG context:	649791
Total unmethylated C's in CHH context:	1568675
Total unmethylated C's in Unknown context:	41846


C methylated in CpG context:	73.7%
C methylated in CHG context:	2.4%
C methylated in CHH context:	5.3%
C methylated in unknown context (CN or CHN):	23.2%


Bismark completed in 0d 0h 1m 35s