Bismark report for: /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_3_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:	48376729
Number of alignments with a unique best hit from the different alignments:	45097
Mapping efficiency:	0.1%
Sequences with no alignments under any condition:	48284321
Sequences did not map uniquely:	47311
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:	11274	((converted) top strand)
CT/GA:	8351	((converted) bottom strand)
GA/CT:	14541	(complementary to (converted) top strand)
GA/GA:	10931	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	411499

Total methylated C's in CpG context:	9538
Total methylated C's in CHG context:	6638
Total methylated C's in CHH context:	92034
Total methylated C's in Unknown context:	0

Total unmethylated C's in CpG context:	13583
Total unmethylated C's in CHG context:	27231
Total unmethylated C's in CHH context:	262475
Total unmethylated C's in Unknown context:	0

C methylated in CpG context:	41.3%
C methylated in CHG context:	19.6%
C methylated in CHH context:	26.0%
Can't determine percentage of methylated Cs in Unknown context (CN or CHN) if value was 0


Bismark completed in 0d 0h 19m 28s