Bismark report for: /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF07-EM01-Zygote_R1_001.fastp-trim.fq.gz and /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF07-EM01-Zygote_R2_001.fastp-trim.fq.gz (version: v0.24.2)
Bismark was run with Bowtie 2 against the bisulfite genome of /gscratch/srlab/kdurkin1/kathleen-coral/project/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:	236542126
Number of paired-end alignments with a unique best hit:	23579759
Mapping efficiency:	10.0% 
Sequence pairs with no alignments under any condition:	202949461
Sequence pairs did not map uniquely:	10012906
Sequence pairs which were discarded because genomic sequence could not be extracted:	53

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	6970090	((converted) top strand)
GA/CT/CT:	4852195	(complementary to (converted) top strand)
GA/CT/GA:	4827905	(complementary to (converted) bottom strand)
CT/GA/GA:	6929516	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	538311693

Total methylated C's in CpG context:	10902218
Total methylated C's in CHG context:	1510834
Total methylated C's in CHH context:	11438727
Total methylated C's in Unknown context:	424447

Total unmethylated C's in CpG context:	57349452
Total unmethylated C's in CHG context:	98086035
Total unmethylated C's in CHH context:	359024427
Total unmethylated C's in Unknown context:	2507832

C methylated in CpG context:	16.0%
C methylated in CHG context:	1.5%
C methylated in CHH context:	3.1%
C methylated in Unknown context (CN or CHN):	14.5%


Bismark completed in 0d 10h 41m 11s