Bismark report for: /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_14_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/v98/ with the specified options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals

Final Alignment report
======================
Sequences analysed in total:	87834637
Number of alignments with a unique best hit from the different alignments:	25416779
Mapping efficiency:	28.9%
Sequences with no alignments under any condition:	26593175
Sequences did not map uniquely:	35824683
Sequences which were discarded because genomic sequence could not be extracted:	0

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	5706998	((converted) top strand)
CT/GA:	5681196	((converted) bottom strand)
GA/CT:	7036812	(complementary to (converted) top strand)
GA/GA:	6991773	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	157858861

Total methylated C's in CpG context:	24048953
Total methylated C's in CHG context:	699575
Total methylated C's in CHH context:	8140563
Total methylated C's in Unknown context:	7073

Total unmethylated C's in CpG context:	4179384
Total unmethylated C's in CHG context:	29973809
Total unmethylated C's in CHH context:	90816577
Total unmethylated C's in Unknown context:	50756

C methylated in CpG context:	85.2%
C methylated in CHG context:	2.3%
C methylated in CHH context:	8.2%
C methylated in Unknown context (CN or CHN):	12.2%


Bismark completed in 0d 1h 56m 27s