Bismark report for: /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_11_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:	54458572
Number of alignments with a unique best hit from the different alignments:	15680143
Mapping efficiency:	28.8%
Sequences with no alignments under any condition:	16326025
Sequences did not map uniquely:	22452404
Sequences which were discarded because genomic sequence could not be extracted:	18576

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	3528573	((converted) top strand)
CT/GA:	3497982	((converted) bottom strand)
GA/CT:	4336953	(complementary to (converted) top strand)
GA/GA:	4298059	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	100296882

Total methylated C's in CpG context:	17662617
Total methylated C's in CHG context:	491939
Total methylated C's in CHH context:	5196171
Total methylated C's in Unknown context:	3246

Total unmethylated C's in CpG context:	2900560
Total unmethylated C's in CHG context:	19823190
Total unmethylated C's in CHH context:	54222405
Total unmethylated C's in Unknown context:	19966

C methylated in CpG context:	85.9%
C methylated in CHG context:	2.4%
C methylated in CHH context:	8.7%
C methylated in Unknown context (CN or CHN):	14.0%


Bismark completed in 0d 1h 9m 17s