Bismark report for: /gscratch/scrubbed/sr320/031520-TG-bs/Meth11_R1_001_val_1.fq.gz and /gscratch/scrubbed/sr320/031520-TG-bs/Meth11_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:	56845589
Number of paired-end alignments with a unique best hit:	676715
Mapping efficiency:	1.2% 
Sequence pairs with no alignments under any condition:	56139484
Sequence pairs did not map uniquely:	29390
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:	150149	((converted) top strand)
GA/CT/CT:	188915	(complementary to (converted) top strand)
GA/CT/GA:	188444	(complementary to (converted) bottom strand)
CT/GA/GA:	149207	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	36266037

Total methylated C's in CpG context:	127853
Total methylated C's in CHG context:	109755
Total methylated C's in CHH context:	238440
Total methylated C's in Unknown context:	13844

Total unmethylated C's in CpG context:	10823684
Total unmethylated C's in CHG context:	9040624
Total unmethylated C's in CHH context:	15925681
Total unmethylated C's in Unknown context:	85814

C methylated in CpG context:	1.2%
C methylated in CHG context:	1.2%
C methylated in CHH context:	1.5%
C methylated in unknown context (CN or CHN):	13.9%


Bismark completed in 0d 0h 56m 28s