Bismark report for: /gscratch/srlab/sr320/data/froger/trim/Mc/Meth16.fastp-trim.202003062412_R1_001.fastq.gz and /gscratch/srlab/sr320/data/froger/trim/Mc/Meth16.fastp-trim.202003062412_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:	71022035
Number of paired-end alignments with a unique best hit:	1575120
Mapping efficiency:	2.2% 
Sequence pairs with no alignments under any condition:	68790096
Sequence pairs did not map uniquely:	656819
Sequence pairs which were discarded because genomic sequence could not be extracted:	30

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	388193	((converted) top strand)
GA/CT/CT:	398871	(complementary to (converted) top strand)
GA/CT/GA:	398181	(complementary to (converted) bottom strand)
CT/GA/GA:	389845	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	73432804

Total methylated C's in CpG context:	1918726
Total methylated C's in CHG context:	205584
Total methylated C's in CHH context:	693863
Total methylated C's in Unknown context:	71104

Total unmethylated C's in CpG context:	10461217
Total unmethylated C's in CHG context:	12864401
Total unmethylated C's in CHH context:	47289013
Total unmethylated C's in Unknown context:	242835

C methylated in CpG context:	15.5%
C methylated in CHG context:	1.6%
C methylated in CHH context:	1.4%
C methylated in unknown context (CN or CHN):	22.6%


Bismark completed in 0d 0h 38m 1s