Bismark report for: /gscratch/scrubbed/sr320/031520-TG-bs/Meth9_R1_001_val_1.fq.gz and /gscratch/scrubbed/sr320/031520-TG-bs/Meth9_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:	87033711
Number of paired-end alignments with a unique best hit:	1702838
Mapping efficiency:	2.0% 
Sequence pairs with no alignments under any condition:	85267224
Sequence pairs did not map uniquely:	63649
Sequence pairs which were discarded because genomic sequence could not be extracted:	0

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	382342	((converted) top strand)
GA/CT/CT:	470912	(complementary to (converted) top strand)
GA/CT/GA:	470618	(complementary to (converted) bottom strand)
CT/GA/GA:	378966	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	93339251

Total methylated C's in CpG context:	371121
Total methylated C's in CHG context:	318297
Total methylated C's in CHH context:	604062
Total methylated C's in Unknown context:	61561

Total unmethylated C's in CpG context:	27272922
Total unmethylated C's in CHG context:	22972831
Total unmethylated C's in CHH context:	41800018
Total unmethylated C's in Unknown context:	286558

C methylated in CpG context:	1.3%
C methylated in CHG context:	1.4%
C methylated in CHH context:	1.4%
C methylated in unknown context (CN or CHN):	17.7%


Bismark completed in 0d 1h 31m 30s