Bismark report for: /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz and /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF01-CM02-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:	133403240
Number of paired-end alignments with a unique best hit:	46656964
Mapping efficiency:	35.0% 
Sequence pairs with no alignments under any condition:	67755480
Sequence pairs did not map uniquely:	18990796
Sequence pairs which were discarded because genomic sequence could not be extracted:	67

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	11335548	((converted) top strand)
GA/CT/CT:	11977584	(complementary to (converted) top strand)
GA/CT/GA:	11985108	(complementary to (converted) bottom strand)
CT/GA/GA:	11358657	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	1511988505

Total methylated C's in CpG context:	42901638
Total methylated C's in CHG context:	6275390
Total methylated C's in CHH context:	27139249
Total methylated C's in Unknown context:	1122139

Total unmethylated C's in CpG context:	190236750
Total unmethylated C's in CHG context:	320201916
Total unmethylated C's in CHH context:	925233562
Total unmethylated C's in Unknown context:	5776506

C methylated in CpG context:	18.4%
C methylated in CHG context:	1.9%
C methylated in CHH context:	2.8%
C methylated in Unknown context (CN or CHN):	16.3%


Bismark completed in 0d 7h 56m 27s