Bismark report for: /gscratch/srlab/sr320/data/froger/trim/Mc/Meth17.fastp-trim.202003063731_R1_001.fastq.gz and /gscratch/srlab/sr320/data/froger/trim/Mc/Meth17.fastp-trim.202003063731_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:	10000000
Number of paired-end alignments with a unique best hit:	2476319
Mapping efficiency:	24.8% 
Sequence pairs with no alignments under any condition:	6446159
Sequence pairs did not map uniquely:	1077522
Sequence pairs which were discarded because genomic sequence could not be extracted:	40

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	605881	((converted) top strand)
GA/CT/CT:	629294	(complementary to (converted) top strand)
GA/CT/GA:	631081	(complementary to (converted) bottom strand)
CT/GA/GA:	610023	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	111833357

Total methylated C's in CpG context:	2705366
Total methylated C's in CHG context:	302915
Total methylated C's in CHH context:	1044685
Total methylated C's in Unknown context:	101022

Total unmethylated C's in CpG context:	16556371
Total unmethylated C's in CHG context:	19708432
Total unmethylated C's in CHH context:	71515588
Total unmethylated C's in Unknown context:	368956

C methylated in CpG context:	14.0%
C methylated in CHG context:	1.5%
C methylated in CHH context:	1.4%
C methylated in unknown context (CN or CHN):	21.5%


Bismark completed in 0d 0h 24m 29s