Bismark report for: input_1.fq.gz (version: v0.22.1)
Option '--directional' specified (default mode): alignments to complementary strands (CTOT, CTOB) were ignored (i.e. not performed)
Bismark was run with Bowtie 2 against the bisulfite genome of /tmp/tmp53fiEn/ with the specified options: -q -L 20 -D 15 -R 2 --score-min L,0,-0.8 --ignore-quals --quiet

Final Alignment report
======================
Sequences analysed in total:	44115
Number of alignments with a unique best hit from the different alignments:	1992
Mapping efficiency:	4.5%
Sequences with no alignments under any condition:	40786
Sequences did not map uniquely:	1337
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:	832	((converted) top strand)
CT/GA:	1160	((converted) bottom strand)
GA/CT:	0	(complementary to (converted) top strand)
GA/GA:	0	(complementary to (converted) bottom strand)

Number of alignments to (merely theoretical) complementary strands being rejected in total:	0

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	31956

Total methylated C's in CpG context:	564
Total methylated C's in CHG context:	249
Total methylated C's in CHH context:	882
Total methylated C's in Unknown context:	36

Total unmethylated C's in CpG context:	608
Total unmethylated C's in CHG context:	6183
Total unmethylated C's in CHH context:	23470
Total unmethylated C's in Unknown context:	232

C methylated in CpG context:	48.1%
C methylated in CHG context:	3.9%
C methylated in CHH context:	3.6%
C methylated in Unknown context (CN or CHN):	13.4%


Bismark completed in 0d 0h 0m 8s