Bismark report for: /gscratch/scrubbed/strigg/analyses/20190806_100K_Salmo_test5bp/AS-0.6/16C_26psu_1_S13_L001_R1_001_val_1.fq.gz_unmapped_reads_1.fq.gz (version: v0.19.0)
Option '--non_directional' specified: alignments to all strands were being performed (OT, OB, CTOT, CTOB)
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

Final Alignment report
======================
Sequences analysed in total:	51367
Number of alignments with a unique best hit from the different alignments:	8232
Mapping efficiency:	16.0%
Sequences with no alignments under any condition:	25002
Sequences did not map uniquely:	18133
Sequences which were discarded because genomic sequence could not be extracted:	1

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	1580	((converted) top strand)
CT/GA:	1623	((converted) bottom strand)
GA/CT:	2540	(complementary to (converted) top strand)
GA/GA:	2488	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	206837

Total methylated C's in CpG context:	13983
Total methylated C's in CHG context:	814
Total methylated C's in CHH context:	6580
Total methylated C's in Unknown context:	530

Total unmethylated C's in CpG context:	5530
Total unmethylated C's in CHG context:	48529
Total unmethylated C's in CHH context:	131401
Total unmethylated C's in Unknown context:	2102

C methylated in CpG context:	71.7%
C methylated in CHG context:	1.6%
C methylated in CHH context:	4.8%
C methylated in Unknown context (CN or CHN):	20.1%


Bismark completed in 0d 0h 0m 53s