Bismark report for: /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_17_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:	42070546
Number of alignments with a unique best hit from the different alignments:	12831686
Mapping efficiency:	30.5%
Sequences with no alignments under any condition:	12357075
Sequences did not map uniquely:	16881785
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:	2921720	((converted) top strand)
CT/GA:	2901018	((converted) bottom strand)
GA/CT:	3516819	(complementary to (converted) top strand)
GA/GA:	3492129	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	79974402

Total methylated C's in CpG context:	12811467
Total methylated C's in CHG context:	384407
Total methylated C's in CHH context:	4482631
Total methylated C's in Unknown context:	3769

Total unmethylated C's in CpG context:	2034144
Total unmethylated C's in CHG context:	16655326
Total unmethylated C's in CHH context:	43606427
Total unmethylated C's in Unknown context:	25194

C methylated in CpG context:	86.3%
C methylated in CHG context:	2.3%
C methylated in CHH context:	9.3%
C methylated in Unknown context (CN or CHN):	13.0%


Bismark completed in 0d 0h 53m 39s