Bismark report for: /gscratch/scrubbed/sr320/031520-TG-bs/Meth18_R1_001_val_1.fq.gz and /gscratch/scrubbed/sr320/031520-TG-bs/Meth18_R2_001_val_2.fq.gz (version: v0.21.0)
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,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500
Option '--non_directional' specified: alignments to all strands were being performed (OT, OB, CTOT, CTOB)

Final Alignment report
======================
Sequence pairs analysed in total:	61585400
Number of paired-end alignments with a unique best hit:	14475532
Mapping efficiency:	23.5% 
Sequence pairs with no alignments under any condition:	46762677
Sequence pairs did not map uniquely:	347191
Sequence pairs which were discarded because genomic sequence could not be extracted:	3

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	3190745	((converted) top strand)
GA/CT/CT:	4071292	(complementary to (converted) top strand)
GA/CT/GA:	4033406	(complementary to (converted) bottom strand)
CT/GA/GA:	3180086	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	843168405

Total methylated C's in CpG context:	3139919
Total methylated C's in CHG context:	2705359
Total methylated C's in CHH context:	4288243
Total methylated C's in Unknown context:	452743

Total unmethylated C's in CpG context:	247647481
Total unmethylated C's in CHG context:	208262441
Total unmethylated C's in CHH context:	377124962
Total unmethylated C's in Unknown context:	2235542

C methylated in CpG context:	1.3%
C methylated in CHG context:	1.3%
C methylated in CHH context:	1.1%
C methylated in unknown context (CN or CHN):	16.8%


Bismark completed in 0d 2h 56m 51s