Bismark report for: /gscratch/scrubbed/sr320/031520-TG-bs/Meth3_R1_001_val_1.fq.gz and /gscratch/scrubbed/sr320/031520-TG-bs/Meth3_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:	77672273
Number of paired-end alignments with a unique best hit:	3476
Mapping efficiency:	0.0% 
Sequence pairs with no alignments under any condition:	77668650
Sequence pairs did not map uniquely:	147
Sequence pairs which were discarded because genomic sequence could not be extracted:	46

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	812	((converted) top strand)
GA/CT/CT:	1039	(complementary to (converted) top strand)
GA/CT/GA:	900	(complementary to (converted) bottom strand)
CT/GA/GA:	679	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	125419

Total methylated C's in CpG context:	5261
Total methylated C's in CHG context:	5705
Total methylated C's in CHH context:	12286
Total methylated C's in Unknown context:	56

Total unmethylated C's in CpG context:	24622
Total unmethylated C's in CHG context:	28136
Total unmethylated C's in CHH context:	49409
Total unmethylated C's in Unknown context:	180

C methylated in CpG context:	17.6%
C methylated in CHG context:	16.9%
C methylated in CHH context:	19.9%
C methylated in unknown context (CN or CHN):	23.7%


Bismark completed in 0d 1h 10m 33s