Bismark report for: S2_PBAT_2_S34_R1_001_val_1.fq.gz and S2_PBAT_2_S34_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:	11983563
Number of paired-end alignments with a unique best hit:	4353540
Mapping efficiency:	36.3% 
Sequence pairs with no alignments under any condition:	6523202
Sequence pairs did not map uniquely:	1106821
Sequence pairs which were discarded because genomic sequence could not be extracted:	105

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	0	((converted) top strand)
GA/CT/CT:	2178387	(complementary to (converted) top strand)
GA/CT/GA:	2175048	(complementary to (converted) bottom strand)
CT/GA/GA:	0	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	105865907

Total methylated C's in CpG context:	2005634
Total methylated C's in CHG context:	529760
Total methylated C's in CHH context:	1198093
Total methylated C's in Unknown context:	423


Total unmethylated C's in CpG context:	21728191
Total unmethylated C's in CHG context:	22197249
Total unmethylated C's in CHH context:	58206980
Total unmethylated C's in Unknown context:	13659


C methylated in CpG context:	8.5%
C methylated in CHG context:	2.3%
C methylated in CHH context:	2.0%
C methylated in unknown context (CN or CHN):	3.0%


Bismark completed in 0d 2h 23m 2s