Bismark report for: ../output/01.00-F-Ptuh-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_POC-50-TP2_S14_R1_001.fastq.gz and ../output/01.00-F-Ptuh-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_POC-50-TP2_S14_R2_001.fastq.gz (version: v0.23.1)
Bismark was run with Bowtie 2 against the bisulfite genome of /scratch3/workspace/zdellaert_uri_edu-deep_dive/deep-dive-expression/F-Ptuh/data/ with the specified options: -q --score-min L,0,-1.0 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500
Option '--non_directional' specified: alignments to all strands were being performed (OT, OB, CTOT, CTOB)

Final Alignment report
======================
Sequence pairs analysed in total:	167114293
Number of paired-end alignments with a unique best hit:	95287182
Mapping efficiency:	57.0% 
Sequence pairs with no alignments under any condition:	44781799
Sequence pairs did not map uniquely:	27045312
Sequence pairs which were discarded because genomic sequence could not be extracted:	87

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	27818348	((converted) top strand)
GA/CT/CT:	21421024	(complementary to (converted) top strand)
GA/CT/GA:	21393822	(complementary to (converted) bottom strand)
CT/GA/GA:	24653901	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	3215206295

Total methylated C's in CpG context:	24480584
Total methylated C's in CHG context:	18188843
Total methylated C's in CHH context:	65242926
Total methylated C's in Unknown context:	6833414

Total unmethylated C's in CpG context:	553212268
Total unmethylated C's in CHG context:	643381408
Total unmethylated C's in CHH context:	1910700266
Total unmethylated C's in Unknown context:	35089127

C methylated in CpG context:	4.2%
C methylated in CHG context:	2.7%
C methylated in CHH context:	3.3%
C methylated in unknown context (CN or CHN):	16.3%


Bismark completed in 0d 11h 26m 2s