Bismark report for: ../../data/03-Peve-bismark/POR-73-TP2_R1_001.fastp-trim.fq.gz and ../../data/03-Peve-bismark/POR-73-TP2_R2_001.fastp-trim.fq.gz (version: v0.24.2)
Bismark was run with Bowtie 2 against the bisulfite genome of /mmfs1/gscratch/srlab/sr320/github/timeseries_molecular/E-Peve/data/ with the specified options: -q --score-min L,0,-0.6 -p 10 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500
Option '--directional' specified (default mode): alignments to complementary strands (CTOT, CTOB) were ignored (i.e. not performed)

Final Alignment report
======================
Sequence pairs analysed in total:	10000
Number of paired-end alignments with a unique best hit:	1088
Mapping efficiency:	10.9% 
Sequence pairs with no alignments under any condition:	8713
Sequence pairs did not map uniquely:	199
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:	524	((converted) top strand)
GA/CT/CT:	0	(complementary to (converted) top strand)
GA/CT/GA:	0	(complementary to (converted) bottom strand)
CT/GA/GA:	564	((converted) bottom strand)

Number of alignments to (merely theoretical) complementary strands being rejected in total:	0

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	55491

Total methylated C's in CpG context:	692
Total methylated C's in CHG context:	17
Total methylated C's in CHH context:	98
Total methylated C's in Unknown context:	0

Total unmethylated C's in CpG context:	8261
Total unmethylated C's in CHG context:	9653
Total unmethylated C's in CHH context:	36770
Total unmethylated C's in Unknown context:	80

C methylated in CpG context:	7.7%
C methylated in CHG context:	0.2%
C methylated in CHH context:	0.3%
C methylated in Unknown context (CN or CHN):	0.0%


Bismark completed in 0d 0h 0m 15s