Bismark report for: /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF02-EM02-Zygote_R1_001.fastp-trim.fq.gz and /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF02-EM02-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:	142822546
Number of paired-end alignments with a unique best hit:	32256397
Mapping efficiency:	22.6% 
Sequence pairs with no alignments under any condition:	95841532
Sequence pairs did not map uniquely:	14724617
Sequence pairs which were discarded because genomic sequence could not be extracted:	49

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	9153439	((converted) top strand)
GA/CT/CT:	7050972	(complementary to (converted) top strand)
GA/CT/GA:	6977351	(complementary to (converted) bottom strand)
CT/GA/GA:	9074586	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	896414654

Total methylated C's in CpG context:	20476573
Total methylated C's in CHG context:	3063299
Total methylated C's in CHH context:	15176232
Total methylated C's in Unknown context:	778818

Total unmethylated C's in CpG context:	110840827
Total unmethylated C's in CHG context:	183025506
Total unmethylated C's in CHH context:	563832217
Total unmethylated C's in Unknown context:	4778053

C methylated in CpG context:	15.6%
C methylated in CHG context:	1.6%
C methylated in CHH context:	2.6%
C methylated in Unknown context (CN or CHN):	14.0%


Bismark completed in 0d 6h 41m 35s