Bismark report for: /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_7_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:	49730113
Number of alignments with a unique best hit from the different alignments:	15462117
Mapping efficiency:	31.1%
Sequences with no alignments under any condition:	14857626
Sequences did not map uniquely:	19410370
Sequences which were discarded because genomic sequence could not be extracted:	14818

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	3528969	((converted) top strand)
CT/GA:	3503854	((converted) bottom strand)
GA/CT:	4227492	(complementary to (converted) top strand)
GA/GA:	4186984	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	94652195

Total methylated C's in CpG context:	12800766
Total methylated C's in CHG context:	441731
Total methylated C's in CHH context:	5214036
Total methylated C's in Unknown context:	2528

Total unmethylated C's in CpG context:	2513676
Total unmethylated C's in CHG context:	18777732
Total unmethylated C's in CHH context:	54904254
Total unmethylated C's in Unknown context:	17310

C methylated in CpG context:	83.6%
C methylated in CHG context:	2.3%
C methylated in CHH context:	8.7%
C methylated in Unknown context (CN or CHN):	12.7%


Bismark completed in 0d 1h 5m 3s