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
=================================
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%
Processed 46462 lines from filtered_Unlabeled_NoIndex_L003_R1.fastq_bismark.sam in total
Total number of methylation call strings processed: 46462
Final Cytosine Methylation Report
=================================
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%