Bismark report for: /gscratch/scrubbed/sr320/031520-TG-bs/Meth13_R1_001_val_1.fq.gz and /gscratch/scrubbed/sr320/031520-TG-bs/Meth13_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:	100607927
Number of paired-end alignments with a unique best hit:	6361993
Mapping efficiency:	6.3% 
Sequence pairs with no alignments under any condition:	93942886
Sequence pairs did not map uniquely:	303048
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:	1557822	((converted) top strand)
GA/CT/CT:	1627505	(complementary to (converted) top strand)
GA/CT/GA:	1623625	(complementary to (converted) bottom strand)
CT/GA/GA:	1553041	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	330622014

Total methylated C's in CpG context:	3076960
Total methylated C's in CHG context:	513693
Total methylated C's in CHH context:	1152918
Total methylated C's in Unknown context:	6198

Total unmethylated C's in CpG context:	102490675
Total unmethylated C's in CHG context:	84959815
Total unmethylated C's in CHH context:	138427953
Total unmethylated C's in Unknown context:	35868

C methylated in CpG context:	2.9%
C methylated in CHG context:	0.6%
C methylated in CHH context:	0.8%
C methylated in unknown context (CN or CHN):	14.7%


Bismark completed in 0d 2h 19m 7s