Bismark report for: /gscratch/srlab/sr320/data/froger/trim/Mc/Meth11.fastp-trim.202003065734_R1_001.fastq.gz and /gscratch/srlab/sr320/data/froger/trim/Mc/Meth11.fastp-trim.202003065734_R2_001.fastq.gz (version: v0.21.0)
Bismark was run with Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/froger/Mcap_Genome/ 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:	55809314
Number of paired-end alignments with a unique best hit:	1753832
Mapping efficiency:	3.1% 
Sequence pairs with no alignments under any condition:	53380684
Sequence pairs did not map uniquely:	674798
Sequence pairs which were discarded because genomic sequence could not be extracted:	29

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	405991	((converted) top strand)
GA/CT/CT:	470482	(complementary to (converted) top strand)
GA/CT/GA:	471496	(complementary to (converted) bottom strand)
CT/GA/GA:	405834	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	81765934

Total methylated C's in CpG context:	1781666
Total methylated C's in CHG context:	188076
Total methylated C's in CHH context:	646329
Total methylated C's in Unknown context:	47916

Total unmethylated C's in CpG context:	12041967
Total unmethylated C's in CHG context:	14571661
Total unmethylated C's in CHH context:	52536235
Total unmethylated C's in Unknown context:	237161

C methylated in CpG context:	12.9%
C methylated in CHG context:	1.3%
C methylated in CHH context:	1.2%
C methylated in unknown context (CN or CHN):	16.8%


Bismark completed in 0d 0h 33m 50s