Bismark report for: /gscratch/scrubbed/samwhite/outputs/20200305_methcompare_fastp_trimming/Meth13.fastp-trim.202003062040_R1_001.fastq.gz and /gscratch/scrubbed/samwhite/outputs/20200305_methcompare_fastp_trimming/Meth13.fastp-trim.202003062040_R2_001.fastq.gz (version: v0.21.0)
Bismark was run with Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/froger/C1_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:	100000
Number of paired-end alignments with a unique best hit:	1763
Mapping efficiency:	1.8% 
Sequence pairs with no alignments under any condition:	96969
Sequence pairs did not map uniquely:	1268
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:	389	((converted) top strand)
GA/CT/CT:	433	(complementary to (converted) top strand)
GA/CT/GA:	475	(complementary to (converted) bottom strand)
CT/GA/GA:	466	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	24183

Total methylated C's in CpG context:	614
Total methylated C's in CHG context:	252
Total methylated C's in CHH context:	9241
Total methylated C's in Unknown context:	153

Total unmethylated C's in CpG context:	919
Total unmethylated C's in CHG context:	1263
Total unmethylated C's in CHH context:	11894
Total unmethylated C's in Unknown context:	223

C methylated in CpG context:	40.1%
C methylated in CHG context:	16.6%
C methylated in CHH context:	43.7%
C methylated in unknown context (CN or CHN):	40.7%


Bismark completed in 0d 0h 1m 18s