Bismark report for: /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_2_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:	46105140
Number of alignments with a unique best hit from the different alignments:	45684
Mapping efficiency:	0.1%
Sequences with no alignments under any condition:	46014221
Sequences did not map uniquely:	45235
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:	11348	((converted) top strand)
CT/GA:	8195	((converted) bottom strand)
GA/CT:	14951	(complementary to (converted) top strand)
GA/GA:	11190	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	413360

Total methylated C's in CpG context:	9582
Total methylated C's in CHG context:	7044
Total methylated C's in CHH context:	101882
Total methylated C's in Unknown context:	0

Total unmethylated C's in CpG context:	13142
Total unmethylated C's in CHG context:	26557
Total unmethylated C's in CHH context:	255153
Total unmethylated C's in Unknown context:	0

C methylated in CpG context:	42.2%
C methylated in CHG context:	21.0%
C methylated in CHH context:	28.5%
Can't determine percentage of methylated Cs in Unknown context (CN or CHN) if value was 0


Bismark completed in 0d 0h 18m 4s