Bismark report for: ../../data/03-Peve-bismark/POR-262-TP4_R1_001.fastp-trim.fq.gz and ../../data/03-Peve-bismark/POR-262-TP4_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 12 --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:	47364179
Number of paired-end alignments with a unique best hit:	29325159
Mapping efficiency:	61.9% 
Sequence pairs with no alignments under any condition:	13996238
Sequence pairs did not map uniquely:	4042782
Sequence pairs which were discarded because genomic sequence could not be extracted:	4976

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	14678288	((converted) top strand)
GA/CT/CT:	0	(complementary to (converted) top strand)
GA/CT/GA:	0	(complementary to (converted) bottom strand)
CT/GA/GA:	14641895	((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:	1455052913

Total methylated C's in CpG context:	20194055
Total methylated C's in CHG context:	1363295
Total methylated C's in CHH context:	5425580
Total methylated C's in Unknown context:	32307

Total unmethylated C's in CpG context:	208900157
Total unmethylated C's in CHG context:	254356912
Total unmethylated C's in CHH context:	964812914
Total unmethylated C's in Unknown context:	1874194

C methylated in CpG context:	8.8%
C methylated in CHG context:	0.5%
C methylated in CHH context:	0.6%
C methylated in Unknown context (CN or CHN):	1.7%


Bismark completed in 0d 3h 25m 23s