Bismark report for: /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_4_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:	44905078
Number of alignments with a unique best hit from the different alignments:	13945808
Mapping efficiency:	31.1%
Sequences with no alignments under any condition:	13481308
Sequences did not map uniquely:	17477962
Sequences which were discarded because genomic sequence could not be extracted:	12622

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	3106857	((converted) top strand)
CT/GA:	3082218	((converted) bottom strand)
GA/CT:	3883121	(complementary to (converted) top strand)
GA/GA:	3860990	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	85421822

Total methylated C's in CpG context:	11788331
Total methylated C's in CHG context:	407048
Total methylated C's in CHH context:	4800476
Total methylated C's in Unknown context:	2127

Total unmethylated C's in CpG context:	1942535
Total unmethylated C's in CHG context:	16959647
Total unmethylated C's in CHH context:	49523785
Total unmethylated C's in Unknown context:	15252

C methylated in CpG context:	85.9%
C methylated in CHG context:	2.3%
C methylated in CHH context:	8.8%
C methylated in Unknown context (CN or CHN):	12.2%


Bismark completed in 0d 0h 59m 31s