Bismark report for: ../output/01.00-E-Peve-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_POR-76-TP2_S6_R1_001.fastq.gz and ../output/01.00-E-Peve-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_POR-76-TP2_S6_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:	173500998
Number of paired-end alignments with a unique best hit:	98546250
Mapping efficiency:	56.8% 
Sequence pairs with no alignments under any condition:	43820661
Sequence pairs did not map uniquely:	31134087
Sequence pairs which were discarded because genomic sequence could not be extracted:	11761

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	28826966	((converted) top strand)
GA/CT/CT:	20227940	(complementary to (converted) top strand)
GA/CT/GA:	20261300	(complementary to (converted) bottom strand)
CT/GA/GA:	29218283	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	3847749515

Total methylated C's in CpG context:	47480036
Total methylated C's in CHG context:	17830772
Total methylated C's in CHH context:	74535138
Total methylated C's in Unknown context:	10391621

Total unmethylated C's in CpG context:	676604903
Total unmethylated C's in CHG context:	737281551
Total unmethylated C's in CHH context:	2294017115
Total unmethylated C's in Unknown context:	38399470

C methylated in CpG context:	6.6%
C methylated in CHG context:	2.4%
C methylated in CHH context:	3.1%
C methylated in unknown context (CN or CHN):	21.3%


Bismark completed in 1d 6h 27m 21s