Bismark report for: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF01-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz and /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF01-CM01-Zygote_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:	32085370
Number of paired-end alignments with a unique best hit:	4232230
Mapping efficiency:	13.2% 
Sequence pairs with no alignments under any condition:	26181125
Sequence pairs did not map uniquely:	1672015
Sequence pairs which were discarded because genomic sequence could not be extracted:	5

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	1143966	((converted) top strand)
GA/CT/CT:	974626	(complementary to (converted) top strand)
GA/CT/GA:	971605	(complementary to (converted) bottom strand)
CT/GA/GA:	1142028	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	118915438

Total methylated C's in CpG context:	2668090
Total methylated C's in CHG context:	562060
Total methylated C's in CHH context:	3117889
Total methylated C's in Unknown context:	168999

Total unmethylated C's in CpG context:	12183733
Total unmethylated C's in CHG context:	21440246
Total unmethylated C's in CHH context:	78943420
Total unmethylated C's in Unknown context:	823411

C methylated in CpG context:	18.0%
C methylated in CHG context:	2.6%
C methylated in CHH context:	3.8%
C methylated in unknown context (CN or CHN):	17.0%


Bismark completed in 0d 0h 57m 22s