Bismark report for: ../../data/CF03-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz and ../../data/CF03-CM04-Larvae_R2_001.fastp-trim.20220827.fq.gz (version: v0.24.2)
Bismark was run with Bowtie 2 against the bisulfite genome of /mmfs1/gscratch/scrubbed/sr320/github/ceasmallr/data/genome/ with the specified options: -q --score-min L,0,-0.6 -p 8 --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:	10000
Number of paired-end alignments with a unique best hit:	4611
Mapping efficiency:	46.1% 
Sequence pairs with no alignments under any condition:	3510
Sequence pairs did not map uniquely:	1879
Sequence pairs which were discarded because genomic sequence could not be extracted:	0

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	1122	((converted) top strand)
GA/CT/CT:	1184	(complementary to (converted) top strand)
GA/CT/GA:	1222	(complementary to (converted) bottom strand)
CT/GA/GA:	1083	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	185545

Total methylated C's in CpG context:	4930
Total methylated C's in CHG context:	670
Total methylated C's in CHH context:	2576
Total methylated C's in Unknown context:	170

Total unmethylated C's in CpG context:	22284
Total unmethylated C's in CHG context:	38689
Total unmethylated C's in CHH context:	116396
Total unmethylated C's in Unknown context:	739

C methylated in CpG context:	18.1%
C methylated in CHG context:	1.7%
C methylated in CHH context:	2.2%
C methylated in Unknown context (CN or CHN):	18.7%


Bismark completed in 0d 0h 0m 16s