Bismark report for: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF03-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/CF03-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:	114639363
Number of paired-end alignments with a unique best hit:	38253850
Mapping efficiency:	33.4% 
Sequence pairs with no alignments under any condition:	61987067
Sequence pairs did not map uniquely:	14398446
Sequence pairs which were discarded because genomic sequence could not be extracted:	28

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	9359769	((converted) top strand)
GA/CT/CT:	9722903	(complementary to (converted) top strand)
GA/CT/GA:	9774279	(complementary to (converted) bottom strand)
CT/GA/GA:	9396871	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	1552465266

Total methylated C's in CpG context:	45560778
Total methylated C's in CHG context:	11557139
Total methylated C's in CHH context:	42165956
Total methylated C's in Unknown context:	2438938

Total unmethylated C's in CpG context:	189329253
Total unmethylated C's in CHG context:	326079297
Total unmethylated C's in CHH context:	937772843
Total unmethylated C's in Unknown context:	8182791

C methylated in CpG context:	19.4%
C methylated in CHG context:	3.4%
C methylated in CHH context:	4.3%
C methylated in unknown context (CN or CHN):	23.0%


Bismark completed in 0d 4h 45m 56s