Bismark report for: /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_6_s456_trimmed.fq (version: v0.21.0)
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/sr320/data/olurida-bs/v082/ with the specified options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals

Final Alignment report
======================
Sequences analysed in total:	46455148
Number of alignments with a unique best hit from the different alignments:	2013278
Mapping efficiency:	4.3%
Sequences with no alignments under any condition:	42132594
Sequences did not map uniquely:	2309276
Sequences which were discarded because genomic sequence could not be extracted:	69

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	403589	((converted) top strand)
CT/GA:	436356	((converted) bottom strand)
GA/CT:	576906	(complementary to (converted) top strand)
GA/GA:	596358	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	12294135

Total methylated C's in CpG context:	1280460
Total methylated C's in CHG context:	56701
Total methylated C's in CHH context:	642287
Total methylated C's in Unknown context:	42

Total unmethylated C's in CpG context:	536403
Total unmethylated C's in CHG context:	2079296
Total unmethylated C's in CHH context:	7698988
Total unmethylated C's in Unknown context:	457

C methylated in CpG context:	70.5%
C methylated in CHG context:	2.7%
C methylated in CHH context:	7.7%
C methylated in Unknown context (CN or CHN):	8.4%


Bismark completed in 0d 0h 23m 54s