Bismark report for: ../../data/EF08-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz and ../../data/EF08-EM04-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:	3602
Mapping efficiency:	36.0% 
Sequence pairs with no alignments under any condition:	4824
Sequence pairs did not map uniquely:	1574
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:	902	((converted) top strand)
GA/CT/CT:	922	(complementary to (converted) top strand)
GA/CT/GA:	936	(complementary to (converted) bottom strand)
CT/GA/GA:	842	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	128257

Total methylated C's in CpG context:	4008
Total methylated C's in CHG context:	778
Total methylated C's in CHH context:	2743
Total methylated C's in Unknown context:	223

Total unmethylated C's in CpG context:	15634
Total unmethylated C's in CHG context:	27621
Total unmethylated C's in CHH context:	77473
Total unmethylated C's in Unknown context:	634

C methylated in CpG context:	20.4%
C methylated in CHG context:	2.7%
C methylated in CHH context:	3.4%
C methylated in Unknown context (CN or CHN):	26.0%


Bismark completed in 0d 0h 0m 16s