Bismark report for: /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_12_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-genomes/v081/ with the specified options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals

Final Alignment report
======================
Sequences analysed in total:	59459431
Number of alignments with a unique best hit from the different alignments:	20145696
Mapping efficiency:	33.9%
Sequences with no alignments under any condition:	17101979
Sequences did not map uniquely:	22211756
Sequences which were discarded because genomic sequence could not be extracted:	16457

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	4509629	((converted) top strand)
CT/GA:	4475635	((converted) bottom strand)
GA/CT:	5594115	(complementary to (converted) top strand)
GA/GA:	5549860	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	120343086

Total methylated C's in CpG context:	13832027
Total methylated C's in CHG context:	461081
Total methylated C's in CHH context:	6664085
Total methylated C's in Unknown context:	2655

Total unmethylated C's in CpG context:	3413355
Total unmethylated C's in CHG context:	24010493
Total unmethylated C's in CHH context:	71962045
Total unmethylated C's in Unknown context:	19915

C methylated in CpG context:	80.2%
C methylated in CHG context:	1.9%
C methylated in CHH context:	8.5%
C methylated in Unknown context (CN or CHN):	11.8%


Bismark completed in 0d 1h 20m 47s