Bismark report for: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF01-EM01-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/EF01-EM01-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:	123554588
Number of paired-end alignments with a unique best hit:	27576783
Mapping efficiency:	22.3% 
Sequence pairs with no alignments under any condition:	86185936
Sequence pairs did not map uniquely:	9791869
Sequence pairs which were discarded because genomic sequence could not be extracted:	47

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	7078183	((converted) top strand)
GA/CT/CT:	6709150	(complementary to (converted) top strand)
GA/CT/GA:	6702209	(complementary to (converted) bottom strand)
CT/GA/GA:	7087194	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	909304877

Total methylated C's in CpG context:	29460680
Total methylated C's in CHG context:	9706738
Total methylated C's in CHH context:	41506141
Total methylated C's in Unknown context:	1767769

Total unmethylated C's in CpG context:	92225935
Total unmethylated C's in CHG context:	175658644
Total unmethylated C's in CHH context:	560746739
Total unmethylated C's in Unknown context:	5418338

C methylated in CpG context:	24.2%
C methylated in CHG context:	5.2%
C methylated in CHH context:	6.9%
C methylated in unknown context (CN or CHN):	24.6%


Bismark completed in 0d 4h 12m 27s