Bismark report for: ../../data/CF01-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz and ../../data/CF01-CM01-Zygote_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,-0.8 -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:	32085370
Number of paired-end alignments with a unique best hit:	5263477
Mapping efficiency:	16.4% 
Sequence pairs with no alignments under any condition:	24901496
Sequence pairs did not map uniquely:	1920397
Sequence pairs which were discarded because genomic sequence could not be extracted:	13

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	1421695	((converted) top strand)
GA/CT/CT:	1213974	(complementary to (converted) top strand)
GA/CT/GA:	1208589	(complementary to (converted) bottom strand)
CT/GA/GA:	1419206	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	147756270

Total methylated C's in CpG context:	3133060
Total methylated C's in CHG context:	761746
Total methylated C's in CHH context:	5081089
Total methylated C's in Unknown context:	323668

Total unmethylated C's in CpG context:	15103667
Total unmethylated C's in CHG context:	26035662
Total unmethylated C's in CHH context:	97641046
Total unmethylated C's in Unknown context:	1696327

C methylated in CpG context:	17.2%
C methylated in CHG context:	2.8%
C methylated in CHH context:	4.9%
C methylated in Unknown context (CN or CHN):	16.0%


Bismark completed in 0d 1h 21m 24s