Bismark report for: sampleA_R1.fastq.gz and sampleA_R2.fastq.gz (version: v0.25.1)
Bismark was run with Bowtie 2 against the bisulfite genome of /genomes/GRCh38/ with the specified options: -q --score-min L,0,-0.2 --ignore-quals

Final Alignment report
======================
Sequence pairs analysed in total:	100000
Number of paired-end alignments with a unique best hit:	82345
Mapping efficiency:	82.35%
Sequence pairs with no alignments under any condition:	12000
Sequence pairs did not map uniquely:	5655
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:	41010	((converted) top strand)
GA/CT/CT:	0	(complementary to (converted) top strand)
GA/CT/GA:	0	(complementary to (converted) bottom strand)
CT/GA/GA:	41335	((converted) bottom strand)

Final Cytosine Methylation Report
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Total number of C's analysed:	4250000

Total methylated C's in CpG context:	210000
Total methylated C's in CHG context:	1500
Total methylated C's in CHH context:	4200

Total unmethylated C's in CpG context:	62000
Total unmethylated C's in CHG context:	1100000
Total unmethylated C's in CHH context:	2872300

C methylated in CpG context:	77.2%
C methylated in CHG context:	0.1%
C methylated in CHH context:	0.1%
