Bismark report for: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF08-CM03-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/CF08-CM03-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:	147000143
Number of paired-end alignments with a unique best hit:	27270023
Mapping efficiency:	18.6% 
Sequence pairs with no alignments under any condition:	108690029
Sequence pairs did not map uniquely:	11040091
Sequence pairs which were discarded because genomic sequence could not be extracted:	30

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	8097427	((converted) top strand)
GA/CT/CT:	5517413	(complementary to (converted) top strand)
GA/CT/GA:	5527808	(complementary to (converted) bottom strand)
CT/GA/GA:	8127345	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	686635733

Total methylated C's in CpG context:	15769913
Total methylated C's in CHG context:	4596366
Total methylated C's in CHH context:	27966021
Total methylated C's in Unknown context:	1028546

Total unmethylated C's in CpG context:	64879675
Total unmethylated C's in CHG context:	118811730
Total unmethylated C's in CHH context:	454612028
Total unmethylated C's in Unknown context:	4664252

C methylated in CpG context:	19.6%
C methylated in CHG context:	3.7%
C methylated in CHH context:	5.8%
C methylated in unknown context (CN or CHN):	18.1%


Bismark completed in 0d 4h 40m 5s