Bismark report for: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF08-CM05-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/CF08-CM05-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:	80683717
Number of paired-end alignments with a unique best hit:	1716695
Mapping efficiency:	2.1% 
Sequence pairs with no alignments under any condition:	78416271
Sequence pairs did not map uniquely:	550751
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:	439115	((converted) top strand)
GA/CT/CT:	418914	(complementary to (converted) top strand)
GA/CT/GA:	418486	(complementary to (converted) bottom strand)
CT/GA/GA:	440180	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	73983804

Total methylated C's in CpG context:	1506054
Total methylated C's in CHG context:	237171
Total methylated C's in CHH context:	1750182
Total methylated C's in Unknown context:	98340

Total unmethylated C's in CpG context:	7890781
Total unmethylated C's in CHG context:	13552439
Total unmethylated C's in CHH context:	49047177
Total unmethylated C's in Unknown context:	339559

C methylated in CpG context:	16.0%
C methylated in CHG context:	1.7%
C methylated in CHH context:	3.4%
C methylated in unknown context (CN or CHN):	22.5%


Bismark completed in 0d 2h 57m 33s