Bismark report for: /Volumes/Bay3/Software/bismark_v0.6.4/filtered_Unlabeled_NoIndex_L003_R1wID_trimmed.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 -k 2 --best --chunkmbs 512

Final Alignment report
======================
Sequences analysed in total:	139660651
Number of alignments with a unique best hit from the different alignments:	7205800
Mapping efficiency:	5.2%
Sequences with no alignments under any condition:	126455782
Sequences did not map uniquely:	3586720
Sequences which were discarded because genomic sequence could not be extracted:	13816

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	3539113	((converted) top strand)
CT/GA:	3666687	((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:	2412349

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	43070400

Total methylated C's in CpG context:	 5173742
Total methylated C's in CHG context:	260101
Total methylated C's in CHH context:	1060970

Total C to T conversions in CpG context:	2571648
Total C to T conversions in CHG context:	7050506
Total C to T conversions in CHH context:	26953433

C methylated in CpG context:	66.8%
C methylated in CHG context:	3.6%
C methylated in CHH context:	3.8%