Bismark report for: /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_5_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/v98/ with the specified options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals

Final Alignment report
======================
Sequences analysed in total:	47401736
Number of alignments with a unique best hit from the different alignments:	15747029
Mapping efficiency:	33.2%
Sequences with no alignments under any condition:	14134741
Sequences did not map uniquely:	17519966
Sequences which were discarded because genomic sequence could not be extracted:	0

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	3575045	((converted) top strand)
CT/GA:	3556303	((converted) bottom strand)
GA/CT:	4329383	(complementary to (converted) top strand)
GA/GA:	4286298	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	93113950

Total methylated C's in CpG context:	9933157
Total methylated C's in CHG context:	400913
Total methylated C's in CHH context:	5646633
Total methylated C's in Unknown context:	3851

Total unmethylated C's in CpG context:	3086035
Total unmethylated C's in CHG context:	18513739
Total unmethylated C's in CHH context:	55533473
Total unmethylated C's in Unknown context:	25960

C methylated in CpG context:	76.3%
C methylated in CHG context:	2.1%
C methylated in CHH context:	9.2%
C methylated in Unknown context (CN or CHN):	12.9%


Bismark completed in 0d 1h 4m 42s