Bismark report for: /gscratch/scrubbed/samwhite/outputs/20200305_methcompare_fastp_trimming/Meth14.fastp-trim.202003064415_R1_001.fastq.gz and /gscratch/scrubbed/samwhite/outputs/20200305_methcompare_fastp_trimming/Meth14.fastp-trim.202003064415_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:	2242
Mapping efficiency:	2.2% 
Sequence pairs with no alignments under any condition:	96217
Sequence pairs did not map uniquely:	1541
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:	450	((converted) top strand)
GA/CT/CT:	623	(complementary to (converted) top strand)
GA/CT/GA:	668	(complementary to (converted) bottom strand)
CT/GA/GA:	501	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	34962

Total methylated C's in CpG context:	1407
Total methylated C's in CHG context:	351
Total methylated C's in CHH context:	11140
Total methylated C's in Unknown context:	140

Total unmethylated C's in CpG context:	1482
Total unmethylated C's in CHG context:	2642
Total unmethylated C's in CHH context:	17940
Total unmethylated C's in Unknown context:	241

C methylated in CpG context:	48.7%
C methylated in CHG context:	11.7%
C methylated in CHH context:	38.3%
C methylated in unknown context (CN or CHN):	36.7%


Bismark completed in 0d 0h 1m 20s