Bismark report for: /gscratch/srlab/sr320/data/olurida-bs/combined.fq.gz (version: v0.22.3)
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/genome/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals

Final Alignment report
======================
Sequences analysed in total:	92334932
Number of alignments with a unique best hit from the different alignments:	43226506
Mapping efficiency:	46.8%
Sequences with no alignments under any condition:	1408355
Sequences did not map uniquely:	47700071
Sequences which were discarded because genomic sequence could not be extracted:	29930

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	16867827	((converted) top strand)
CT/GA:	16848105	((converted) bottom strand)
GA/CT:	4733711	(complementary to (converted) top strand)
GA/GA:	4746933	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	244706621

Total methylated C's in CpG context:	8302900
Total methylated C's in CHG context:	1148320
Total methylated C's in CHH context:	26772276
Total methylated C's in Unknown context:	465478

Total unmethylated C's in CpG context:	20955820
Total unmethylated C's in CHG context:	38244673
Total unmethylated C's in CHH context:	149282632
Total unmethylated C's in Unknown context:	808211

C methylated in CpG context:	28.4%
C methylated in CHG context:	2.9%
C methylated in CHH context:	15.2%
C methylated in Unknown context (CN or CHN):	36.5%


Bismark completed in 0d 3h 0m 56s