Bismark report for: ../../data/EF03-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz and ../../data/EF03-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:	3043
Mapping efficiency:	30.4% 
Sequence pairs with no alignments under any condition:	5738
Sequence pairs did not map uniquely:	1219
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:	863	((converted) top strand)
GA/CT/CT:	727	(complementary to (converted) top strand)
GA/CT/GA:	663	(complementary to (converted) bottom strand)
CT/GA/GA:	790	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	109586

Total methylated C's in CpG context:	3528
Total methylated C's in CHG context:	1267
Total methylated C's in CHH context:	4428
Total methylated C's in Unknown context:	190

Total unmethylated C's in CpG context:	12081
Total unmethylated C's in CHG context:	22373
Total unmethylated C's in CHH context:	65909
Total unmethylated C's in Unknown context:	610

C methylated in CpG context:	22.6%
C methylated in CHG context:	5.4%
C methylated in CHH context:	6.3%
C methylated in Unknown context (CN or CHN):	23.8%


Bismark completed in 0d 0h 0m 15s