Bismark report for: /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF07-EM03-Larvae_R1_001.fastp-trim.fq.gz and /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF07-EM03-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:	128061872
Number of paired-end alignments with a unique best hit:	42132656
Mapping efficiency:	32.9% 
Sequence pairs with no alignments under any condition:	70148503
Sequence pairs did not map uniquely:	15780713
Sequence pairs which were discarded because genomic sequence could not be extracted:	44

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	10067430	((converted) top strand)
GA/CT/CT:	10973939	(complementary to (converted) top strand)
GA/CT/GA:	11003713	(complementary to (converted) bottom strand)
CT/GA/GA:	10087530	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	1472676037

Total methylated C's in CpG context:	38937577
Total methylated C's in CHG context:	4763094
Total methylated C's in CHH context:	20707519
Total methylated C's in Unknown context:	766513

Total unmethylated C's in CpG context:	173273221
Total unmethylated C's in CHG context:	302035165
Total unmethylated C's in CHH context:	932959461
Total unmethylated C's in Unknown context:	5448077

C methylated in CpG context:	18.3%
C methylated in CHG context:	1.6%
C methylated in CHH context:	2.2%
C methylated in Unknown context (CN or CHN):	12.3%


Bismark completed in 0d 11h 11m 11s