Bismark report for: /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_2_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:	46105140
Number of alignments with a unique best hit from the different alignments:	14822810
Mapping efficiency:	32.2%
Sequences with no alignments under any condition:	14100920
Sequences did not map uniquely:	17181410
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:	3308195	((converted) top strand)
CT/GA:	3289743	((converted) bottom strand)
GA/CT:	4126694	(complementary to (converted) top strand)
GA/GA:	4098178	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	89520561

Total methylated C's in CpG context:	11404907
Total methylated C's in CHG context:	408791
Total methylated C's in CHH context:	5222368
Total methylated C's in Unknown context:	3817

Total unmethylated C's in CpG context:	2330389
Total unmethylated C's in CHG context:	17926332
Total unmethylated C's in CHH context:	52227774
Total unmethylated C's in Unknown context:	25383

C methylated in CpG context:	83.0%
C methylated in CHG context:	2.2%
C methylated in CHH context:	9.1%
C methylated in Unknown context (CN or CHN):	13.1%


Bismark completed in 0d 1h 2m 15s