Bismark report for: /gscratch/scrubbed/sr320/031520-TG-bs/Meth6_R1_001_val_1.fq.gz and /gscratch/scrubbed/sr320/031520-TG-bs/Meth6_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/lambda/ 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:	140382105
Number of paired-end alignments with a unique best hit:	45458
Mapping efficiency:	0.0% 
Sequence pairs with no alignments under any condition:	140336393
Sequence pairs did not map uniquely:	254
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:	11842	((converted) top strand)
GA/CT/CT:	12391	(complementary to (converted) top strand)
GA/CT/GA:	11168	(complementary to (converted) bottom strand)
CT/GA/GA:	10057	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	1096087

Total methylated C's in CpG context:	14788
Total methylated C's in CHG context:	5207
Total methylated C's in CHH context:	68878
Total methylated C's in Unknown context:	13

Total unmethylated C's in CpG context:	259934
Total unmethylated C's in CHG context:	303368
Total unmethylated C's in CHH context:	443912
Total unmethylated C's in Unknown context:	739

C methylated in CpG context:	5.4%
C methylated in CHG context:	1.7%
C methylated in CHH context:	13.4%
C methylated in unknown context (CN or CHN):	1.7%


Bismark completed in 0d 2h 6m 25s