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-bs/v082/ 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:	2533316
Mapping efficiency:	4.7%
Sequences with no alignments under any condition:	49708344
Sequences did not map uniquely:	2216912
Sequences which were discarded because genomic sequence could not be extracted:	60

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	526236	((converted) top strand)
CT/GA:	570358	((converted) bottom strand)
GA/CT:	693851	(complementary to (converted) top strand)
GA/GA:	742811	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	15943045

Total methylated C's in CpG context:	3143225
Total methylated C's in CHG context:	96153
Total methylated C's in CHH context:	702171
Total methylated C's in Unknown context:	141

Total unmethylated C's in CpG context:	717521
Total unmethylated C's in CHG context:	2746405
Total unmethylated C's in CHH context:	8537570
Total unmethylated C's in Unknown context:	281

C methylated in CpG context:	81.4%
C methylated in CHG context:	3.4%
C methylated in CHH context:	7.6%
C methylated in Unknown context (CN or CHN):	33.4%


Bismark completed in 0d 0h 27m 56s