Bismark report for: /gscratch/scrubbed/samwhite/outputs/20200305_methcompare_fastp_trimming/Meth4.fastp-trim.202003062011_R1_001.fastq.gz and /gscratch/scrubbed/samwhite/outputs/20200305_methcompare_fastp_trimming/Meth4.fastp-trim.202003062011_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:	4262
Mapping efficiency:	4.3% 
Sequence pairs with no alignments under any condition:	93615
Sequence pairs did not map uniquely:	2123
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:	1025	((converted) top strand)
GA/CT/CT:	1147	(complementary to (converted) top strand)
GA/CT/GA:	1115	(complementary to (converted) bottom strand)
CT/GA/GA:	975	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	110873

Total methylated C's in CpG context:	7471
Total methylated C's in CHG context:	593
Total methylated C's in CHH context:	16130
Total methylated C's in Unknown context:	189

Total unmethylated C's in CpG context:	14206
Total unmethylated C's in CHG context:	14528
Total unmethylated C's in CHH context:	57945
Total unmethylated C's in Unknown context:	640

C methylated in CpG context:	34.5%
C methylated in CHG context:	3.9%
C methylated in CHH context:	21.8%
C methylated in unknown context (CN or CHN):	22.8%


Bismark completed in 0d 0h 1m 20s