Bismark report for: /gscratch/scrubbed/samwhite/outputs/20200305_methcompare_fastp_trimming/Meth1.fastp-trim.202003061245_R1_001.fastq.gz and /gscratch/scrubbed/samwhite/outputs/20200305_methcompare_fastp_trimming/Meth1.fastp-trim.202003061245_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:	1159
Mapping efficiency:	1.2% 
Sequence pairs with no alignments under any condition:	98699
Sequence pairs did not map uniquely:	142
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:	252	((converted) top strand)
GA/CT/CT:	341	(complementary to (converted) top strand)
GA/CT/GA:	305	(complementary to (converted) bottom strand)
CT/GA/GA:	261	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	54702

Total methylated C's in CpG context:	6128
Total methylated C's in CHG context:	316
Total methylated C's in CHH context:	2521
Total methylated C's in Unknown context:	43

Total unmethylated C's in CpG context:	1570
Total unmethylated C's in CHG context:	10277
Total unmethylated C's in CHH context:	33890
Total unmethylated C's in Unknown context:	169

C methylated in CpG context:	79.6%
C methylated in CHG context:	3.0%
C methylated in CHH context:	6.9%
C methylated in unknown context (CN or CHN):	20.3%


Bismark completed in 0d 0h 1m 21s