Bismark report for: /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF05-EM06-Larvae_R1_001.fastp-trim.fq.gz and /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF05-EM06-Larvae_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:	197315016
Number of paired-end alignments with a unique best hit:	69096435
Mapping efficiency:	35.0% 
Sequence pairs with no alignments under any condition:	106977420
Sequence pairs did not map uniquely:	21241161
Sequence pairs which were discarded because genomic sequence could not be extracted:	35

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	16463519	((converted) top strand)
GA/CT/CT:	18062442	(complementary to (converted) top strand)
GA/CT/GA:	18070671	(complementary to (converted) bottom strand)
CT/GA/GA:	16499768	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	2770765034

Total methylated C's in CpG context:	75491086
Total methylated C's in CHG context:	24300011
Total methylated C's in CHH context:	100612703
Total methylated C's in Unknown context:	1879039

Total unmethylated C's in CpG context:	306626655
Total unmethylated C's in CHG context:	515819901
Total unmethylated C's in CHH context:	1747914678
Total unmethylated C's in Unknown context:	10676837

C methylated in CpG context:	19.8%
C methylated in CHG context:	4.5%
C methylated in CHH context:	5.4%
C methylated in Unknown context (CN or CHN):	15.0%


Bismark completed in 0d 13h 27m 13s