Bismark report for: /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_10_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:	78221457
Number of alignments with a unique best hit from the different alignments:	25374001
Mapping efficiency:	32.4%
Sequences with no alignments under any condition:	21899233
Sequences did not map uniquely:	30948223
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:	6511929	((converted) top strand)
CT/GA:	6446118	((converted) bottom strand)
GA/CT:	6239306	(complementary to (converted) top strand)
GA/GA:	6176648	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	159318003

Total methylated C's in CpG context:	24571414
Total methylated C's in CHG context:	738291
Total methylated C's in CHH context:	8532254
Total methylated C's in Unknown context:	7636

Total unmethylated C's in CpG context:	4429949
Total unmethylated C's in CHG context:	33811864
Total unmethylated C's in CHH context:	87234231
Total unmethylated C's in Unknown context:	52101

C methylated in CpG context:	84.7%
C methylated in CHG context:	2.1%
C methylated in CHH context:	8.9%
C methylated in Unknown context (CN or CHN):	12.8%


Bismark completed in 0d 1h 45m 27s