Bismark report for: /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_18_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:	55048106
Number of alignments with a unique best hit from the different alignments:	18170956
Mapping efficiency:	33.0%
Sequences with no alignments under any condition:	15404219
Sequences did not map uniquely:	21472931
Sequences which were discarded because genomic sequence could not be extracted:	16272

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	3982167	((converted) top strand)
CT/GA:	3955904	((converted) bottom strand)
GA/CT:	5128139	(complementary to (converted) top strand)
GA/GA:	5088474	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	109733028

Total methylated C's in CpG context:	14029679
Total methylated C's in CHG context:	448447
Total methylated C's in CHH context:	5906339
Total methylated C's in Unknown context:	2550

Total unmethylated C's in CpG context:	2832392
Total unmethylated C's in CHG context:	22328360
Total unmethylated C's in CHH context:	64187811
Total unmethylated C's in Unknown context:	18670

C methylated in CpG context:	83.2%
C methylated in CHG context:	2.0%
C methylated in CHH context:	8.4%
C methylated in Unknown context (CN or CHN):	12.0%


Bismark completed in 0d 1h 14m 26s