Bismark report for: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF03-EM03-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/EF03-EM03-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:	135271836
Number of paired-end alignments with a unique best hit:	22016467
Mapping efficiency:	16.3% 
Sequence pairs with no alignments under any condition:	103804735
Sequence pairs did not map uniquely:	9450634
Sequence pairs which were discarded because genomic sequence could not be extracted:	21

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	6178649	((converted) top strand)
GA/CT/CT:	4793827	(complementary to (converted) top strand)
GA/CT/GA:	4822688	(complementary to (converted) bottom strand)
CT/GA/GA:	6221282	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	581355521

Total methylated C's in CpG context:	15352387
Total methylated C's in CHG context:	5077870
Total methylated C's in CHH context:	25138967
Total methylated C's in Unknown context:	1140538

Total unmethylated C's in CpG context:	56233493
Total unmethylated C's in CHG context:	104518461
Total unmethylated C's in CHH context:	375034343
Total unmethylated C's in Unknown context:	4116576

C methylated in CpG context:	21.4%
C methylated in CHG context:	4.6%
C methylated in CHH context:	6.3%
C methylated in unknown context (CN or CHN):	21.7%


Bismark completed in 0d 4h 2m 45s