Bismark report for: BSR2_1.fq.trimmed.single
Bowtie was run against the bisulfite genome of /home/bioinformatics2/data/pseudochromosome/chrV2/ZmB73_RefGen_v2/bs_reference_for_bsseeker/ with the specified options: -q --phred64-quals -n 2 -l 28 -k 2 --best --chunkmbs 512

Final Alignment report
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Sequences analysed in total:	85306770
Number of alignments with a unique best hit from the different alignments:	36528719
Mapping efficiency:	42.8%
Sequences with no alignments under any condition:	3508004
Sequences did not map uniquely:	45270047

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	18240698	((converted) top strand)
CT/GA:	18258593	((converted) bottom strand)
GA/CT:	15200	(complementary to (converted) bottom strand)
GA/GA:	14228	(complementary to (converted) top strand)

Final Cytosine Methylation Report
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Total number of C's analysed:	689827326

Total methylated C's in CpG context:	 90252576
Total methylated C's in CHG context:	68512286
Total methylated C's in CHH context:	7434639

Total C to T conversions in CpG context:	34525665
Total C to T conversions in CHG context:	48862435
Total C to T conversions in CHH context:	440239725

C methylated in CpG context:	72.3%
C methylated in CHG context:	58.4%
C methylated in CHH context:	1.7%