Bismark report for: /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_5_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:	47401736
Number of alignments with a unique best hit from the different alignments:	15838795
Mapping efficiency:	33.4%
Sequences with no alignments under any condition:	13874948
Sequences did not map uniquely:	17687993
Sequences which were discarded because genomic sequence could not be extracted:	13185

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	3592897	((converted) top strand)
CT/GA:	3571645	((converted) bottom strand)
GA/CT:	4352516	(complementary to (converted) top strand)
GA/GA:	4308552	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	93616428

Total methylated C's in CpG context:	9995135
Total methylated C's in CHG context:	402878
Total methylated C's in CHH context:	5641348
Total methylated C's in Unknown context:	2165

Total unmethylated C's in CpG context:	3094855
Total unmethylated C's in CHG context:	18627231
Total unmethylated C's in CHH context:	55854981
Total unmethylated C's in Unknown context:	15434

C methylated in CpG context:	76.4%
C methylated in CHG context:	2.1%
C methylated in CHH context:	9.2%
C methylated in Unknown context (CN or CHN):	12.3%


Bismark completed in 0d 1h 5m 8s