Bismark report for: /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz and /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF02-CM02-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:	206045849
Number of paired-end alignments with a unique best hit:	27528519
Mapping efficiency:	13.4% 
Sequence pairs with no alignments under any condition:	167768755
Sequence pairs did not map uniquely:	10748575
Sequence pairs which were discarded because genomic sequence could not be extracted:	43

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	8331198	((converted) top strand)
GA/CT/CT:	5401679	(complementary to (converted) top strand)
GA/CT/GA:	5415702	(complementary to (converted) bottom strand)
CT/GA/GA:	8379897	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	560662988

Total methylated C's in CpG context:	13245595
Total methylated C's in CHG context:	4402157
Total methylated C's in CHH context:	28851821
Total methylated C's in Unknown context:	583161

Total unmethylated C's in CpG context:	50988738
Total unmethylated C's in CHG context:	92569772
Total unmethylated C's in CHH context:	370604905
Total unmethylated C's in Unknown context:	3089401

C methylated in CpG context:	20.6%
C methylated in CHG context:	4.5%
C methylated in CHH context:	7.2%
C methylated in Unknown context (CN or CHN):	15.9%


Bismark completed in 0d 10h 47m 23s