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/chr1-29MT/ 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:	34354958
Number of paired-end alignments with a unique best hit:	17189300
Mapping efficiency:	50.0% 
Sequence pairs with no alignments under any condition:	12268288
Sequence pairs did not map uniquely:	4897370
Sequence pairs which were discarded because genomic sequence could not be extracted:	6

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	4365205	((converted) top strand)
GA/CT/CT:	4195722	(complementary to (converted) top strand)
GA/CT/GA:	4231609	(complementary to (converted) bottom strand)
CT/GA/GA:	4396758	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	752835717

Total methylated C's in CpG context:	55344843
Total methylated C's in CHG context:	2267266
Total methylated C's in CHH context:	12548155
Total methylated C's in Unknown context:	974936


Total unmethylated C's in CpG context:	17178938
Total unmethylated C's in CHG context:	187219912
Total unmethylated C's in CHH context:	478276603
Total unmethylated C's in Unknown context:	2473945


C methylated in CpG context:	76.3%
C methylated in CHG context:	1.2%
C methylated in CHH context:	2.6%
C methylated in unknown context (CN or CHN):	28.3%


Bismark completed in 0d 3h 38m 35s