Bismark report for: /gscratch/scrubbed/samwhite/outputs/20200305_methcompare_fastp_trimming/Meth2.fastp-trim.202003062630_R1_001.fastq.gz and /gscratch/scrubbed/samwhite/outputs/20200305_methcompare_fastp_trimming/Meth2.fastp-trim.202003062630_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:	1696
Mapping efficiency:	1.7% 
Sequence pairs with no alignments under any condition:	98097
Sequence pairs did not map uniquely:	207
Sequence pairs which were discarded because genomic sequence could not be extracted:	1

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	378	((converted) top strand)
GA/CT/CT:	463	(complementary to (converted) top strand)
GA/CT/GA:	510	(complementary to (converted) bottom strand)
CT/GA/GA:	344	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	78606

Total methylated C's in CpG context:	9028
Total methylated C's in CHG context:	524
Total methylated C's in CHH context:	3424
Total methylated C's in Unknown context:	89

Total unmethylated C's in CpG context:	1764
Total unmethylated C's in CHG context:	14663
Total unmethylated C's in CHH context:	49203
Total unmethylated C's in Unknown context:	218

C methylated in CpG context:	83.7%
C methylated in CHG context:	3.5%
C methylated in CHH context:	6.5%
C methylated in unknown context (CN or CHN):	29.0%


Bismark completed in 0d 0h 1m 19s