Bismark report for: /gscratch/scrubbed/strigg/TRIMG_adapt_5bp/TRIM_cat/16C_32psu_3_S3_R1_001_val_1.fq.gz and /gscratch/scrubbed/strigg/TRIMG_adapt_5bp/TRIM_cat/16C_32psu_3_S3_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:	27293279
Number of paired-end alignments with a unique best hit:	14077908
Mapping efficiency:	51.6% 
Sequence pairs with no alignments under any condition:	7639032
Sequence pairs did not map uniquely:	5576339
Sequence pairs which were discarded because genomic sequence could not be extracted:	1641

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	3758456	((converted) top strand)
GA/CT/CT:	3263750	(complementary to (converted) top strand)
GA/CT/GA:	3278875	(complementary to (converted) bottom strand)
CT/GA/GA:	3775186	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	562213851

Total methylated C's in CpG context:	42389529
Total methylated C's in CHG context:	1897697
Total methylated C's in CHH context:	10650157
Total methylated C's in Unknown context:	790890


Total unmethylated C's in CpG context:	13177716
Total unmethylated C's in CHG context:	143348150
Total unmethylated C's in CHH context:	350750602
Total unmethylated C's in Unknown context:	1719039


C methylated in CpG context:	76.3%
C methylated in CHG context:	1.3%
C methylated in CHH context:	2.9%
C methylated in unknown context (CN or CHN):	31.5%


Bismark completed in 0d 3h 8m 57s