Bismark report for: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF03-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz and /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF03-EM05-Larvae_R2_001.fastp-trim.20220827.fq.gz (version: v0.24.0)
Bismark was run with Bowtie 2 against the bisulfite genome of /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/data/Cvirginica_v300/ with the specified options: -q --score-min L,0,-0.6 -p 4 --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:	137327090
Number of paired-end alignments with a unique best hit:	38448483
Mapping efficiency:	28.0% 
Sequence pairs with no alignments under any condition:	85109571
Sequence pairs did not map uniquely:	13769036
Sequence pairs which were discarded because genomic sequence could not be extracted:	24

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	9542483	((converted) top strand)
GA/CT/CT:	9632776	(complementary to (converted) top strand)
GA/CT/GA:	9686749	(complementary to (converted) bottom strand)
CT/GA/GA:	9586451	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	1464329898

Total methylated C's in CpG context:	42838919
Total methylated C's in CHG context:	11647536
Total methylated C's in CHH context:	44584075
Total methylated C's in Unknown context:	2508195

Total unmethylated C's in CpG context:	170100170
Total unmethylated C's in CHG context:	297885534
Total unmethylated C's in CHH context:	897273664
Total unmethylated C's in Unknown context:	8216535

C methylated in CpG context:	20.1%
C methylated in CHG context:	3.8%
C methylated in CHH context:	4.7%
C methylated in unknown context (CN or CHN):	23.4%


Bismark completed in 0d 5h 22m 20s