Bismark report for: S1_1.fastq.gz and S1_2.fastq.gz (version: v0.24.1)
Bismark was run with Bowtie 2 against the bisulfite genome of /refs/GRCh38/ with the specified options: -q --score-min L,0,-0.2 -p 4
Option '--directional' specified (default mode): alignments to complementary strands (CTOT, CTOB) were ignored (i.e. not performed)

Final Alignment report
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Sequence pairs analysed in total:	1000000
Number of paired-end alignments with a unique best hit:	789000
Mapping efficiency:	78.9%
Sequence pairs with no alignments under any condition:	150000
Sequence pairs did not map uniquely:	61000
Sequence pairs which were discarded because genomic sequence could not be extracted:	0

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	394500	((converted) top strand)
GA/CT/CT:	0	(complementary to (converted) top strand)
GA/CT/GA:	0	(complementary to (converted) bottom strand)
CT/GA/GA:	394500	((converted) bottom strand)

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

Final Cytosine Methylation Report
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Total number of C's analysed:	20500000

Total methylated C's in CpG context:	3200000
Total methylated C's in CHG context:	42000
Total methylated C's in CHH context:	61000
Total methylated C's in Unknown context (CN or CHN):	1800

Total unmethylated C's in CpG context:	1100000
Total unmethylated C's in CHG context:	7900000
Total unmethylated C's in CHH context:	8197000
Total unmethylated C's in Unknown context (CN or CHN):	18200

C methylated in CpG context:	74.4%
C methylated in CHG context:	0.5%
C methylated in CHH context:	0.7%
C methylated in unknown context (CN or CHN):	9.0%

Bismark completed in 0d 1h 12m 4s
