Bismark report for: /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_6_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:	46455148
Number of alignments with a unique best hit from the different alignments:	15623039
Mapping efficiency:	33.6%
Sequences with no alignments under any condition:	13764452
Sequences did not map uniquely:	17067657
Sequences which were discarded because genomic sequence could not be extracted:	12143

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	3476758	((converted) top strand)
CT/GA:	3459999	((converted) bottom strand)
GA/CT:	4353366	(complementary to (converted) top strand)
GA/GA:	4320773	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	91279017

Total methylated C's in CpG context:	9068779
Total methylated C's in CHG context:	406529
Total methylated C's in CHH context:	5393062
Total methylated C's in Unknown context:	1851

Total unmethylated C's in CpG context:	2345574
Total unmethylated C's in CHG context:	17647340
Total unmethylated C's in CHH context:	56417733
Total unmethylated C's in Unknown context:	15035

C methylated in CpG context:	79.5%
C methylated in CHG context:	2.3%
C methylated in CHH context:	8.7%
C methylated in Unknown context (CN or CHN):	11.0%


Bismark completed in 0d 1h 5m 6s