Bismark report for: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF05-EM05-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/EF05-EM05-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:	121477726
Number of paired-end alignments with a unique best hit:	8664305
Mapping efficiency:	7.1% 
Sequence pairs with no alignments under any condition:	108244447
Sequence pairs did not map uniquely:	4568974
Sequence pairs which were discarded because genomic sequence could not be extracted:	16

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	2257139	((converted) top strand)
GA/CT/CT:	2069633	(complementary to (converted) top strand)
GA/CT/GA:	2073793	(complementary to (converted) bottom strand)
CT/GA/GA:	2263724	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	198057902

Total methylated C's in CpG context:	3391868
Total methylated C's in CHG context:	893353
Total methylated C's in CHH context:	5515515
Total methylated C's in Unknown context:	260010

Total unmethylated C's in CpG context:	22417388
Total unmethylated C's in CHG context:	36063675
Total unmethylated C's in CHH context:	129776103
Total unmethylated C's in Unknown context:	1878448

C methylated in CpG context:	13.1%
C methylated in CHG context:	2.4%
C methylated in CHH context:	4.1%
C methylated in unknown context (CN or CHN):	12.2%


Bismark completed in 0d 3h 45m 38s