Bismark report for: /gscratch/scrubbed/sr320/031520-TG-bs/Meth15_R1_001_val_1.fq.gz and /gscratch/scrubbed/sr320/031520-TG-bs/Meth15_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:	108911247
Number of paired-end alignments with a unique best hit:	9108570
Mapping efficiency:	8.4% 
Sequence pairs with no alignments under any condition:	99342731
Sequence pairs did not map uniquely:	459946
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:	2199593	((converted) top strand)
GA/CT/CT:	2351436	(complementary to (converted) top strand)
GA/CT/GA:	2355183	(complementary to (converted) bottom strand)
CT/GA/GA:	2202358	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	466793413

Total methylated C's in CpG context:	4433012
Total methylated C's in CHG context:	713048
Total methylated C's in CHH context:	1663938
Total methylated C's in Unknown context:	8878

Total unmethylated C's in CpG context:	144957150
Total unmethylated C's in CHG context:	120042295
Total unmethylated C's in CHH context:	194983970
Total unmethylated C's in Unknown context:	48293

C methylated in CpG context:	3.0%
C methylated in CHG context:	0.6%
C methylated in CHH context:	0.8%
C methylated in unknown context (CN or CHN):	15.5%


Bismark completed in 0d 2h 43m 48s