Bismark report for: /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_all_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:	605809374
Number of alignments with a unique best hit from the different alignments:	532554
Mapping efficiency:	0.1%
Sequences with no alignments under any condition:	604756951
Sequences did not map uniquely:	519869
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:	132066	((converted) top strand)
CT/GA:	97991	((converted) bottom strand)
GA/CT:	170121	(complementary to (converted) top strand)
GA/GA:	132376	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	4742693

Total methylated C's in CpG context:	129843
Total methylated C's in CHG context:	74534
Total methylated C's in CHH context:	1017146
Total methylated C's in Unknown context:	0

Total unmethylated C's in CpG context:	163526
Total unmethylated C's in CHG context:	332272
Total unmethylated C's in CHH context:	3025372
Total unmethylated C's in Unknown context:	0

C methylated in CpG context:	44.3%
C methylated in CHG context:	18.3%
C methylated in CHH context:	25.2%
Can't determine percentage of methylated Cs in Unknown context (CN or CHN) if value was 0


Bismark completed in 0d 4h 1m 5s