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-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:	44905078
Number of alignments with a unique best hit from the different alignments:	2010139
Mapping efficiency:	4.5%
Sequences with no alignments under any condition:	40784777
Sequences did not map uniquely:	2110162
Sequences which were discarded because genomic sequence could not be extracted:	74

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	407301	((converted) top strand)
CT/GA:	439778	((converted) bottom strand)
GA/CT:	568615	(complementary to (converted) top strand)
GA/GA:	594371	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	12404965

Total methylated C's in CpG context:	1806777
Total methylated C's in CHG context:	69275
Total methylated C's in CHH context:	620239
Total methylated C's in Unknown context:	50

Total unmethylated C's in CpG context:	510473
Total unmethylated C's in CHG context:	2191210
Total unmethylated C's in CHH context:	7206991
Total unmethylated C's in Unknown context:	290

C methylated in CpG context:	78.0%
C methylated in CHG context:	3.1%
C methylated in CHH context:	7.9%
C methylated in Unknown context (CN or CHN):	14.7%


Bismark completed in 0d 0h 23m 2s