Bismark report for: /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_14_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/ecoli-MG1655/ with the specified options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals

Final Alignment report
======================
Sequences analysed in total:	87834637
Number of alignments with a unique best hit from the different alignments:	73054
Mapping efficiency:	0.1%
Sequences with no alignments under any condition:	87680345
Sequences did not map uniquely:	81238
Sequences which were discarded because genomic sequence could not be extracted:	0

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	18485	((converted) top strand)
CT/GA:	13548	((converted) bottom strand)
GA/CT:	23389	(complementary to (converted) top strand)
GA/GA:	17632	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	662534

Total methylated C's in CpG context:	17289
Total methylated C's in CHG context:	9397
Total methylated C's in CHH context:	123380
Total methylated C's in Unknown context:	0

Total unmethylated C's in CpG context:	22945
Total unmethylated C's in CHG context:	47531
Total unmethylated C's in CHH context:	441992
Total unmethylated C's in Unknown context:	0

C methylated in CpG context:	43.0%
C methylated in CHG context:	16.5%
C methylated in CHH context:	21.8%
Can't determine percentage of methylated Cs in Unknown context (CN or CHN) if value was 0


Bismark completed in 0d 0h 34m 58s