Bismark report for: /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_13_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:	64352550
Number of alignments with a unique best hit from the different alignments:	19721209
Mapping efficiency:	30.6%
Sequences with no alignments under any condition:	18442450
Sequences did not map uniquely:	26188891
Sequences which were discarded because genomic sequence could not be extracted:	20168

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	4410505	((converted) top strand)
CT/GA:	4370600	((converted) bottom strand)
GA/CT:	5484879	(complementary to (converted) top strand)
GA/GA:	5435057	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	123608897

Total methylated C's in CpG context:	19125117
Total methylated C's in CHG context:	556295
Total methylated C's in CHH context:	6410972
Total methylated C's in Unknown context:	3425

Total unmethylated C's in CpG context:	3215880
Total unmethylated C's in CHG context:	24861808
Total unmethylated C's in CHH context:	69438825
Total unmethylated C's in Unknown context:	22722

C methylated in CpG context:	85.6%
C methylated in CHG context:	2.2%
C methylated in CHH context:	8.5%
C methylated in Unknown context (CN or CHN):	13.1%


Bismark completed in 0d 1h 23m 45s