Bismark report for: ../output/01.00-E-Peve-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_POR-71-TP2_S9_R1_001.fastq.gz and ../output/01.00-E-Peve-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_POR-71-TP2_S9_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:	236709796
Number of paired-end alignments with a unique best hit:	132052904
Mapping efficiency:	55.8% 
Sequence pairs with no alignments under any condition:	66375041
Sequence pairs did not map uniquely:	38281851
Sequence pairs which were discarded because genomic sequence could not be extracted:	17665

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	34407731	((converted) top strand)
GA/CT/CT:	31419253	(complementary to (converted) top strand)
GA/CT/GA:	31482943	(complementary to (converted) bottom strand)
CT/GA/GA:	34725312	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	5285849436

Total methylated C's in CpG context:	69970819
Total methylated C's in CHG context:	19181560
Total methylated C's in CHH context:	91424567
Total methylated C's in Unknown context:	11983188

Total unmethylated C's in CpG context:	900501437
Total unmethylated C's in CHG context:	1011829797
Total unmethylated C's in CHH context:	3192941256
Total unmethylated C's in Unknown context:	62425874

C methylated in CpG context:	7.2%
C methylated in CHG context:	1.9%
C methylated in CHH context:	2.8%
C methylated in unknown context (CN or CHN):	16.1%


Bismark completed in 1d 19h 26m 56s