Bismark report for: /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF04-EM04-Zygote_R1_001.fastp-trim.fq.gz and /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF04-EM04-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:	156051705
Number of paired-end alignments with a unique best hit:	13101846
Mapping efficiency:	8.4% 
Sequence pairs with no alignments under any condition:	137152854
Sequence pairs did not map uniquely:	5797005
Sequence pairs which were discarded because genomic sequence could not be extracted:	39

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	3227099	((converted) top strand)
GA/CT/CT:	3293198	(complementary to (converted) top strand)
GA/CT/GA:	3327067	(complementary to (converted) bottom strand)
CT/GA/GA:	3254443	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	277701930

Total methylated C's in CpG context:	6445114
Total methylated C's in CHG context:	2039614
Total methylated C's in CHH context:	9515860
Total methylated C's in Unknown context:	462087

Total unmethylated C's in CpG context:	30876926
Total unmethylated C's in CHG context:	50171833
Total unmethylated C's in CHH context:	178652583
Total unmethylated C's in Unknown context:	2103819

C methylated in CpG context:	17.3%
C methylated in CHG context:	3.9%
C methylated in CHH context:	5.1%
C methylated in Unknown context (CN or CHN):	18.0%


Bismark completed in 0d 6h 59m 32s