Bismark report for: /gscratch/scrubbed/strigg/analyses/20190806_100K_Salmo_test5bp/16C_26psu_1_S13_L001_R1_001_val_1.fq.gz and /gscratch/scrubbed/strigg/analyses/20190806_100K_Salmo_test5bp/16C_26psu_1_S13_L001_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:	100000
Number of paired-end alignments with a unique best hit:	48633
Mapping efficiency:	48.6% 
Sequence pairs with no alignments under any condition:	34055
Sequence pairs did not map uniquely:	17312
Sequence pairs which were discarded because genomic sequence could not be extracted:	9

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	12521	((converted) top strand)
GA/CT/CT:	11738	(complementary to (converted) top strand)
GA/CT/GA:	11785	(complementary to (converted) bottom strand)
CT/GA/GA:	12580	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	2128840

Total methylated C's in CpG context:	160096
Total methylated C's in CHG context:	6381
Total methylated C's in CHH context:	30862
Total methylated C's in Unknown context:	2753


Total unmethylated C's in CpG context:	50751
Total unmethylated C's in CHG context:	531950
Total unmethylated C's in CHH context:	1348800
Total unmethylated C's in Unknown context:	7073


C methylated in CpG context:	75.9%
C methylated in CHG context:	1.2%
C methylated in CHH context:	2.2%
C methylated in unknown context (CN or CHN):	28.0%


Bismark completed in 0d 0h 1m 26s