Bismark report for: /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_1_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:	46792286
Number of alignments with a unique best hit from the different alignments:	2117445
Mapping efficiency:	4.5%
Sequences with no alignments under any condition:	42430582
Sequences did not map uniquely:	2244259
Sequences which were discarded because genomic sequence could not be extracted:	52

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	432543	((converted) top strand)
CT/GA:	474012	((converted) bottom strand)
GA/CT:	585370	(complementary to (converted) top strand)
GA/GA:	625468	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	13077617

Total methylated C's in CpG context:	1860212
Total methylated C's in CHG context:	70565
Total methylated C's in CHH context:	647883
Total methylated C's in Unknown context:	68

Total unmethylated C's in CpG context:	609554
Total unmethylated C's in CHG context:	2297560
Total unmethylated C's in CHH context:	7591843
Total unmethylated C's in Unknown context:	342

C methylated in CpG context:	75.3%
C methylated in CHG context:	3.0%
C methylated in CHH context:	7.9%
C methylated in Unknown context (CN or CHN):	16.6%


Bismark completed in 0d 0h 24m 0s