Bismark report for: ../data/22-Apul-meth/ACR-140-TP2_R1.fastp-trim.fq.gz and ../data/22-Apul-meth/ACR-140-TP2_R2.fastp-trim.fq.gz (version: v0.24.0)
Bismark was run with Bowtie 2 against the bisulfite genome of /home/shared/8TB_HDD_03/sr320/github/deep-dive-expression/D-Apul/data/ with the specified options: -q --score-min L,0,-1.0 -p 10 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500
Option '--directional' specified (default mode): alignments to complementary strands (CTOT, CTOB) were ignored (i.e. not performed)

Final Alignment report
======================
Sequence pairs analysed in total:	253164476
Number of paired-end alignments with a unique best hit:	473894
Mapping efficiency:	0.2% 
Sequence pairs with no alignments under any condition:	252531245
Sequence pairs did not map uniquely:	159337
Sequence pairs which were discarded because genomic sequence could not be extracted:	0

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	231705	((converted) top strand)
GA/CT/CT:	0	(complementary to (converted) top strand)
GA/CT/GA:	0	(complementary to (converted) bottom strand)
CT/GA/GA:	242189	((converted) bottom strand)

Number of alignments to (merely theoretical) complementary strands being rejected in total:	0

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	10273551

Total methylated C's in CpG context:	765854
Total methylated C's in CHG context:	555949
Total methylated C's in CHH context:	4532164
Total methylated C's in Unknown context:	57277

Total unmethylated C's in CpG context:	734199
Total unmethylated C's in CHG context:	754999
Total unmethylated C's in CHH context:	2930386
Total unmethylated C's in Unknown context:	108119

C methylated in CpG context:	51.1%
C methylated in CHG context:	42.4%
C methylated in CHH context:	60.7%
C methylated in unknown context (CN or CHN):	34.6%


Bismark completed in 0d 4h 56m 28s