Bismark report for: /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF03-EM03-Zygote_R1_001.fastp-trim.REPAIRED.fq.gz and /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF03-EM03-Zygote_R2_001.fastp-trim.REPAIRED.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:	133337327
Number of paired-end alignments with a unique best hit:	21524633
Mapping efficiency:	16.1% 
Sequence pairs with no alignments under any condition:	103555667
Sequence pairs did not map uniquely:	8257027
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:	6049554	((converted) top strand)
GA/CT/CT:	4687480	(complementary to (converted) top strand)
GA/CT/GA:	4703312	(complementary to (converted) bottom strand)
CT/GA/GA:	6084266	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	492559811

Total methylated C's in CpG context:	12916237
Total methylated C's in CHG context:	3461459
Total methylated C's in CHH context:	19406022
Total methylated C's in Unknown context:	595330

Total unmethylated C's in CpG context:	47347964
Total unmethylated C's in CHG context:	87279346
Total unmethylated C's in CHH context:	322148783
Total unmethylated C's in Unknown context:	2693339

C methylated in CpG context:	21.4%
C methylated in CHG context:	3.8%
C methylated in CHH context:	5.7%
C methylated in Unknown context (CN or CHN):	18.1%


Bismark completed in 0d 6h 41m 33s