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,-0.6 -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:	16975867
Mapping efficiency:	49.4% 
Sequence pairs with no alignments under any condition:	11400230
Sequence pairs did not map uniquely:	5978861
Sequence pairs which were discarded because genomic sequence could not be extracted:	1964

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	4316125	((converted) top strand)
GA/CT/CT:	4145375	(complementary to (converted) top strand)
GA/CT/GA:	4174149	(complementary to (converted) bottom strand)
CT/GA/GA:	4338254	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	743440841

Total methylated C's in CpG context:	54903499
Total methylated C's in CHG context:	2218723
Total methylated C's in CHH context:	12206626
Total methylated C's in Unknown context:	961446


Total unmethylated C's in CpG context:	16575990
Total unmethylated C's in CHG context:	185279605
Total unmethylated C's in CHH context:	472256398
Total unmethylated C's in Unknown context:	2380618


C methylated in CpG context:	76.8%
C methylated in CHG context:	1.2%
C methylated in CHH context:	2.5%
C methylated in unknown context (CN or CHN):	28.8%


Bismark completed in 0d 4h 3m 27s