Bismark report for: data/3_TTAGGC_L001_R1_001.fastq.gz (version: v0.19.0)
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 /Volumes/Orange_block/wd/18-06-13/genome/ with the specified options: -q --score-min L,0,-0.9 -p 4 --reorder --ignore-quals

Final Alignment report
======================
Sequences analysed in total:	1000
Number of alignments with a unique best hit from the different alignments:	624
Mapping efficiency:	62.4%
Sequences with no alignments under any condition:	88
Sequences did not map uniquely:	288
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:	282	((converted) top strand)
CT/GA:	299	((converted) bottom strand)
GA/CT:	23	(complementary to (converted) top strand)
GA/GA:	19	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	5581

Total methylated C's in CpG context:	257
Total methylated C's in CHG context:	58
Total methylated C's in CHH context:	288
Total methylated C's in Unknown context:	11

Total unmethylated C's in CpG context:	668
Total unmethylated C's in CHG context:	1044
Total unmethylated C's in CHH context:	3266
Total unmethylated C's in Unknown context:	41

C methylated in CpG context:	27.8%
C methylated in CHG context:	5.3%
C methylated in CHH context:	8.1%
C methylated in Unknown context (CN or CHN):	21.2%


Bismark completed in 0d 0h 1m 43s