Bismark report for: /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_15_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:	67984205
Number of alignments with a unique best hit from the different alignments:	3168995
Mapping efficiency:	4.7%
Sequences with no alignments under any condition:	61719035
Sequences did not map uniquely:	3096175
Sequences which were discarded because genomic sequence could not be extracted:	60

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	659615	((converted) top strand)
CT/GA:	718002	((converted) bottom strand)
GA/CT:	858524	(complementary to (converted) top strand)
GA/GA:	932794	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	19698902

Total methylated C's in CpG context:	3595616
Total methylated C's in CHG context:	120168
Total methylated C's in CHH context:	904169
Total methylated C's in Unknown context:	115

Total unmethylated C's in CpG context:	814267
Total unmethylated C's in CHG context:	3500880
Total unmethylated C's in CHH context:	10763802
Total unmethylated C's in Unknown context:	368

C methylated in CpG context:	81.5%
C methylated in CHG context:	3.3%
C methylated in CHH context:	7.7%
C methylated in Unknown context (CN or CHN):	23.8%


Bismark completed in 0d 0h 34m 45s