Bismark report for: /gscratch/scrubbed/strigg/analyses/20190806_100K_Salmo_test5bp/AS-0.6/16C_26psu_1_S13_L001_R2_001_val_2.fq.gz_unmapped_reads_2.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:	7113
Mapping efficiency:	13.8%
Sequences with no alignments under any condition:	26265
Sequences did not map uniquely:	17989
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:	1281	((converted) top strand)
CT/GA:	1207	((converted) bottom strand)
GA/CT:	2267	(complementary to (converted) top strand)
GA/GA:	2357	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	189153

Total methylated C's in CpG context:	12213
Total methylated C's in CHG context:	670
Total methylated C's in CHH context:	6516
Total methylated C's in Unknown context:	482

Total unmethylated C's in CpG context:	4733
Total unmethylated C's in CHG context:	41746
Total unmethylated C's in CHH context:	123275
Total unmethylated C's in Unknown context:	1985

C methylated in CpG context:	72.1%
C methylated in CHG context:	1.6%
C methylated in CHH context:	5.0%
C methylated in Unknown context (CN or CHN):	19.5%


Bismark completed in 0d 0h 0m 59s