Bismark report for: BSR1_1_1.fq.trimmed.paired1 and BSR1_1_1.fq.trimmed.paired2
Bowtie was run against the bisulfite genome of /home/bioinformatics2/data/bismark_index/ with the specified options: -q --phred64-quals -n 2 -l 28 -e 100 -k 2 --best --minins 50 --maxins 550 --chunkmbs 512

Option '--directional' specified: alignments to complementary strands will be ignored
Final Alignment report
======================
Number of paired-end alignments with a unique best hit:	56819646
Mapping efficiency:	63.9% 
Sequences with no alignments under any condition:	7794380
Sequences did not map uniquely:	24315299

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	28587181	((converted) top strand)
GA/CT/GA:	0	(complementary to (converted) top strand)
GA/CT/CT:	0	(complementary to (converted) bottom strand)
CT/GA/GA:	28232465	((converted) bottom strand)

Number of alignments to (merely theoretical) complementary strands being rejected in total:	16564

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	2222006259

Total methylated C's in CpG context:	321380895
Total methylated C's in CHG context:	248390737
Total methylated C's in CHH context:	20423223

Total C to T conversions in CpG context:	95730361
Total C to T conversions in CHG context:	135462511
Total C to T conversions in CHH context:	1400618532

C methylated in CpG context:	77.0%
C methylated in CHG context:	64.7%
C methylated in CHH context:	1.4%