Bismark report for: /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_all_s456_trimmed.fq (version: v0.21.0)
Option '--non_directional' specified: alignments to all strands were being performed (OT, OB, CTOT, CTOB)
Bismark was run with Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/olurida-bs/v082/ with the specified options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals

Final Alignment report
======================
Sequences analysed in total:	605809374
Number of alignments with a unique best hit from the different alignments:	27806680
Mapping efficiency:	4.6%
Sequences with no alignments under any condition:	550394238
Sequences did not map uniquely:	27608456
Sequences which were discarded because genomic sequence could not be extracted:	671

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	5864343	((converted) top strand)
CT/GA:	6330145	((converted) bottom strand)
GA/CT:	7523167	(complementary to (converted) top strand)
GA/GA:	8088354	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	172354157

Total methylated C's in CpG context:	27953676
Total methylated C's in CHG context:	967507
Total methylated C's in CHH context:	8116739
Total methylated C's in Unknown context:	972

Total unmethylated C's in CpG context:	7703035
Total unmethylated C's in CHG context:	30588122
Total unmethylated C's in CHH context:	97025078
Total unmethylated C's in Unknown context:	3699

C methylated in CpG context:	78.4%
C methylated in CHG context:	3.1%
C methylated in CHH context:	7.7%
C methylated in Unknown context (CN or CHN):	20.8%


Bismark completed in 0d 5h 9m 54s