Bismark report for: ../output/01.00-E-Peve-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_POR-73-TP2_S7_R1_001.fastq.gz and ../output/01.00-E-Peve-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_POR-73-TP2_S7_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:	102561868
Number of paired-end alignments with a unique best hit:	61680314
Mapping efficiency:	60.1% 
Sequence pairs with no alignments under any condition:	29688557
Sequence pairs did not map uniquely:	11192997
Sequence pairs which were discarded because genomic sequence could not be extracted:	11356

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	18614980	((converted) top strand)
GA/CT/CT:	12216738	(complementary to (converted) top strand)
GA/CT/GA:	12220945	(complementary to (converted) bottom strand)
CT/GA/GA:	18616295	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	2962310396

Total methylated C's in CpG context:	38310421
Total methylated C's in CHG context:	9626500
Total methylated C's in CHH context:	43218935
Total methylated C's in Unknown context:	7482071

Total unmethylated C's in CpG context:	463611232
Total unmethylated C's in CHG context:	549194379
Total unmethylated C's in CHH context:	1858348929
Total unmethylated C's in Unknown context:	24226368

C methylated in CpG context:	7.6%
C methylated in CHG context:	1.7%
C methylated in CHH context:	2.3%
C methylated in unknown context (CN or CHN):	23.6%


Bismark completed in 0d 21h 54m 38s