Bismark report for: /gscratch/srlab/sr320/data/olurida-bs/2_CGATGT_L001_R1_001_trimmed.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:	11654467
Number of alignments with a unique best hit from the different alignments:	5433833
Mapping efficiency:	46.6%
Sequences with no alignments under any condition:	191064
Sequences did not map uniquely:	6029570
Sequences which were discarded because genomic sequence could not be extracted:	3794

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	2119792	((converted) top strand)
CT/GA:	2115564	((converted) bottom strand)
GA/CT:	596380	(complementary to (converted) top strand)
GA/GA:	598303	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	30793506

Total methylated C's in CpG context:	1054675
Total methylated C's in CHG context:	176932
Total methylated C's in CHH context:	3415378
Total methylated C's in Unknown context:	57018

Total unmethylated C's in CpG context:	2614904
Total unmethylated C's in CHG context:	4783710
Total unmethylated C's in CHH context:	18747907
Total unmethylated C's in Unknown context:	99509

C methylated in CpG context:	28.7%
C methylated in CHG context:	3.6%
C methylated in CHH context:	15.4%
C methylated in Unknown context (CN or CHN):	36.4%


Bismark completed in 0d 0h 23m 19s