Bismark report for: filtered_Unlabeled_NoIndex_L003_R1.fastq
Option '--directional' specified: alignments to complementary strands will be ignored
Bowtie was run against the bisulfite genome of /Volumes/Bay3/Software/bismark_v0.6.4/genomes/ with the specified options: -q -n 1 -l 50 -k 2 --best --chunkmbs 512

Final Alignment report
======================
Sequences analysed in total:	139728554
Number of alignments with a unique best hit from the different alignments:	46463
Mapping efficiency:	0.0%
Sequences with no alignments under any condition:	139581084
Sequences did not map uniquely:	91544
Sequences which were discarded because genomic sequence could not be extracted:	1

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	23771	((converted) top strand)
CT/GA:	22692	((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:	9463

Final Cytosine Methylation Report
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Total number of C's analysed:	327062

Total methylated C's in CpG context:	 51012
Total methylated C's in CHG context:	905
Total methylated C's in CHH context:	5502

Total C to T conversions in CpG context:	18901
Total C to T conversions in CHG context:	32500
Total C to T conversions in CHH context:	218242

C methylated in CpG context:	73.0%
C methylated in CHG context:	2.7%
C methylated in CHH context:	2.5%