Bismark report for: /gscratch/scrubbed/sr320/031520-TG-bs/Meth10_R1_001_val_1.fq.gz and /gscratch/scrubbed/sr320/031520-TG-bs/Meth10_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:	83382907
Number of paired-end alignments with a unique best hit:	4575
Mapping efficiency:	0.0% 
Sequence pairs with no alignments under any condition:	83378138
Sequence pairs did not map uniquely:	194
Sequence pairs which were discarded because genomic sequence could not be extracted:	27

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	1100	((converted) top strand)
GA/CT/CT:	1269	(complementary to (converted) top strand)
GA/CT/GA:	1181	(complementary to (converted) bottom strand)
CT/GA/GA:	998	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	156842

Total methylated C's in CpG context:	767
Total methylated C's in CHG context:	1049
Total methylated C's in CHH context:	6714
Total methylated C's in Unknown context:	22

Total unmethylated C's in CpG context:	36472
Total unmethylated C's in CHG context:	39789
Total unmethylated C's in CHH context:	72051
Total unmethylated C's in Unknown context:	233

C methylated in CpG context:	2.1%
C methylated in CHG context:	2.6%
C methylated in CHH context:	8.5%
C methylated in unknown context (CN or CHN):	8.6%


Bismark completed in 0d 1h 15m 37s