Bismark report for: ../data/22-Apul-meth/ACR-150-TP2_R1.fastp-trim.fq.gz and ../data/22-Apul-meth/ACR-150-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:	233529125
Number of paired-end alignments with a unique best hit:	455080
Mapping efficiency:	0.2% 
Sequence pairs with no alignments under any condition:	232911156
Sequence pairs did not map uniquely:	162889
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:	222794	((converted) top strand)
GA/CT/CT:	0	(complementary to (converted) top strand)
GA/CT/GA:	0	(complementary to (converted) bottom strand)
CT/GA/GA:	232286	((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:	9465098

Total methylated C's in CpG context:	721196
Total methylated C's in CHG context:	547496
Total methylated C's in CHH context:	4267634
Total methylated C's in Unknown context:	55005

Total unmethylated C's in CpG context:	662934
Total unmethylated C's in CHG context:	690342
Total unmethylated C's in CHH context:	2575496
Total unmethylated C's in Unknown context:	94368

C methylated in CpG context:	52.1%
C methylated in CHG context:	44.2%
C methylated in CHH context:	62.4%
C methylated in unknown context (CN or CHN):	36.8%


Bismark completed in 0d 4h 24m 56s