Bismark report for: /gscratch/srlab/sr320/data/olurida-bs/3_TTAGGC_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:	11555321
Number of alignments with a unique best hit from the different alignments:	5436861
Mapping efficiency:	47.1%
Sequences with no alignments under any condition:	173630
Sequences did not map uniquely:	5944830
Sequences which were discarded because genomic sequence could not be extracted:	3707

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	2126775	((converted) top strand)
CT/GA:	2119608	((converted) bottom strand)
GA/CT:	592511	(complementary to (converted) top strand)
GA/GA:	594260	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	30884657

Total methylated C's in CpG context:	1070977
Total methylated C's in CHG context:	141123
Total methylated C's in CHH context:	3362649
Total methylated C's in Unknown context:	59075

Total unmethylated C's in CpG context:	2690299
Total unmethylated C's in CHG context:	4839624
Total unmethylated C's in CHH context:	18779985
Total unmethylated C's in Unknown context:	102723

C methylated in CpG context:	28.5%
C methylated in CHG context:	2.8%
C methylated in CHH context:	15.2%
C methylated in Unknown context (CN or CHN):	36.5%


Bismark completed in 0d 0h 23m 2s