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/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:	56845589
Number of paired-end alignments with a unique best hit:	2005
Mapping efficiency:	0.0% 
Sequence pairs with no alignments under any condition:	56843442
Sequence pairs did not map uniquely:	142
Sequence pairs which were discarded because genomic sequence could not be extracted:	11

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	447	((converted) top strand)
GA/CT/CT:	590	(complementary to (converted) top strand)
GA/CT/GA:	513	(complementary to (converted) bottom strand)
CT/GA/GA:	444	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	53723

Total methylated C's in CpG context:	355
Total methylated C's in CHG context:	388
Total methylated C's in CHH context:	4221
Total methylated C's in Unknown context:	17

Total unmethylated C's in CpG context:	11141
Total unmethylated C's in CHG context:	12277
Total unmethylated C's in CHH context:	25341
Total unmethylated C's in Unknown context:	114

C methylated in CpG context:	3.1%
C methylated in CHG context:	3.1%
C methylated in CHH context:	14.3%
C methylated in unknown context (CN or CHN):	13.0%


Bismark completed in 0d 0h 51m 50s