Bismark report for: /gscratch/srlab/sr320/data/olurida-bs//zr1394_10_s456_trimmed.fq.gz (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 14 --reorder --ignore-quals

Final Alignment report
======================
Sequences analysed in total:	78221457
Number of alignments with a unique best hit from the different alignments:	25462569
Mapping efficiency:	32.6%
Sequences with no alignments under any condition:	21496817
Sequences did not map uniquely:	31262071
Sequences which were discarded because genomic sequence could not be extracted:	30186

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	6528162	((converted) top strand)
CT/GA:	6453340	((converted) bottom strand)
GA/CT:	6260193	(complementary to (converted) top strand)
GA/GA:	6190688	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	159765962

Total methylated C's in CpG context:	24639901
Total methylated C's in CHG context:	738394
Total methylated C's in CHH context:	8517097
Total methylated C's in Unknown context:	4229

Total unmethylated C's in CpG context:	4431826
Total unmethylated C's in CHG context:	33913328
Total unmethylated C's in CHH context:	87525416
Total unmethylated C's in Unknown context:	27106

C methylated in CpG context:	84.8%
C methylated in CHG context:	2.1%
C methylated in CHH context:	8.9%
C methylated in Unknown context (CN or CHN):	13.5%


Bismark completed in 0d 5h 37m 12s