Bismark report for: S2_PBAT_1_S33_R1_001_val_1.fq.gz and S2_PBAT_1_S33_R2_001_val_2.fq.gz (version: v0.19.0)
Bismark was run with Bowtie 2 against the bisulfite genome of /oak/stanford/groups/akundaje/marinovg/genomes/dm6/bismarck_indexes-BT2/ with the specified options: -q --score-min L,0,-0.2 --ignore-quals --no-mixed --no-discordant --dovetail --maxins 1000
Option '--pbat' specified: alignments to original strands (OT, OB) were ignored (i.e. not performed)

Final Alignment report
======================
Sequence pairs analysed in total:	4601131
Number of paired-end alignments with a unique best hit:	1560441
Mapping efficiency:	33.9% 
Sequence pairs with no alignments under any condition:	2645081
Sequence pairs did not map uniquely:	395609
Sequence pairs which were discarded because genomic sequence could not be extracted:	32

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	0	((converted) top strand)
GA/CT/CT:	779831	(complementary to (converted) top strand)
GA/CT/GA:	780578	(complementary to (converted) bottom strand)
CT/GA/GA:	0	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	37851461

Total methylated C's in CpG context:	634933
Total methylated C's in CHG context:	174937
Total methylated C's in CHH context:	392562
Total methylated C's in Unknown context:	166


Total unmethylated C's in CpG context:	7956115
Total unmethylated C's in CHG context:	7999787
Total unmethylated C's in CHH context:	20693127
Total unmethylated C's in Unknown context:	4777


C methylated in CpG context:	7.4%
C methylated in CHG context:	2.1%
C methylated in CHH context:	1.9%
C methylated in unknown context (CN or CHN):	3.4%


Bismark completed in 0d 0h 53m 20s