./bismark -n 1 -l 50 ./genome/  /Volumes/Bay3/Software/bismark_v0.7.12/filtered_174gm_A_ACTGATA_L002_R1.fastq --path_to_bowtie /Volumes/Bay3/Software/bowtie/  

Final Alignment report

======================

Sequences analysed in total:     139728554

Number of alignments with a unique best hit from the different alignments:     67921027

Mapping efficiency:     48.6%

Sequences with no alignments under any condition:     30305071

Sequences did not map uniquely:     41502456

Sequences which were discarded because genomic sequence could not be extracted:     1479

Number of sequences with unique best (first) alignment came from the bowtie output:

CT/CT:     33952273     ((converted) top strand)

CT/GA:     33968754     ((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:     0

Final Cytosine Methylation Report

=================================

Total number of C's analysed:     400492170

Total methylated C's in CpG context:     40216579

Total methylated C's in CHG context:     2091401

Total methylated C's in CHH context:     10298637

Total C to T conversions in CpG context:     18992872

Total C to T conversions in CHG context:     71913795

Total C to T conversions in CHH context:     256978886

C methylated in CpG context:     67.9%

C methylated in CHG context:     2.8%

C methylated in CHH context:     3.9%

genefish:bismark_v0.7.12 Steven$