Bismark report for: /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_9_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:	77350922
Number of alignments with a unique best hit from the different alignments:	25240310
Mapping efficiency:	32.6%
Sequences with no alignments under any condition:	22010659
Sequences did not map uniquely:	30099953
Sequences which were discarded because genomic sequence could not be extracted:	1

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	5674291	((converted) top strand)
CT/GA:	5647087	((converted) bottom strand)
GA/CT:	6980377	(complementary to (converted) top strand)
GA/GA:	6938554	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	150063744

Total methylated C's in CpG context:	16646053
Total methylated C's in CHG context:	573090
Total methylated C's in CHH context:	8128400
Total methylated C's in Unknown context:	5241

Total unmethylated C's in CpG context:	4057189
Total unmethylated C's in CHG context:	28845101
Total unmethylated C's in CHH context:	91813911
Total unmethylated C's in Unknown context:	42803

C methylated in CpG context:	80.4%
C methylated in CHG context:	1.9%
C methylated in CHH context:	8.1%
C methylated in Unknown context (CN or CHN):	10.9%


Bismark completed in 0d 1h 47m 17s