Bismark report for: ../output/01.00-E-Peve-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_POR-79-TP2_S10_R1_001.fastq.gz and ../output/01.00-E-Peve-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_POR-79-TP2_S10_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/E-Peve/data/ with the specified options: -q --score-min L,0,-1.0 -p 48 --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:	267531009
Number of paired-end alignments with a unique best hit:	147058074
Mapping efficiency:	55.0% 
Sequence pairs with no alignments under any condition:	79040089
Sequence pairs did not map uniquely:	41432846
Sequence pairs which were discarded because genomic sequence could not be extracted:	19080

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	38049264	((converted) top strand)
GA/CT/CT:	35288060	(complementary to (converted) top strand)
GA/CT/GA:	35314264	(complementary to (converted) bottom strand)
CT/GA/GA:	38387406	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	6007547193

Total methylated C's in CpG context:	81514938
Total methylated C's in CHG context:	22267955
Total methylated C's in CHH context:	104025447
Total methylated C's in Unknown context:	14712308

Total unmethylated C's in CpG context:	1013411203
Total unmethylated C's in CHG context:	1141944448
Total unmethylated C's in CHH context:	3644383202
Total unmethylated C's in Unknown context:	73888265

C methylated in CpG context:	7.4%
C methylated in CHG context:	1.9%
C methylated in CHH context:	2.8%
C methylated in unknown context (CN or CHN):	16.6%


Bismark completed in 1d 17h 14m 11s