Bismark report for: ../output/01.00-F-Ptuh-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_POC-47-TP2_S13_R1_001.fastq.gz and ../output/01.00-F-Ptuh-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_POC-47-TP2_S13_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:	151987190
Number of paired-end alignments with a unique best hit:	90000133
Mapping efficiency:	59.2% 
Sequence pairs with no alignments under any condition:	38018588
Sequence pairs did not map uniquely:	23968469
Sequence pairs which were discarded because genomic sequence could not be extracted:	93

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	25028895	((converted) top strand)
GA/CT/CT:	20880873	(complementary to (converted) top strand)
GA/CT/GA:	20847563	(complementary to (converted) bottom strand)
CT/GA/GA:	23242709	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	3022744266

Total methylated C's in CpG context:	21446654
Total methylated C's in CHG context:	15194531
Total methylated C's in CHH context:	62636135
Total methylated C's in Unknown context:	7115726

Total unmethylated C's in CpG context:	516406005
Total unmethylated C's in CHG context:	602797818
Total unmethylated C's in CHH context:	1804263123
Total unmethylated C's in Unknown context:	35351450

C methylated in CpG context:	4.0%
C methylated in CHG context:	2.5%
C methylated in CHH context:	3.4%
C methylated in unknown context (CN or CHN):	16.8%


Bismark completed in 0d 11h 8m 24s