Bismark report for: /gscratch/scrubbed/strigg/analyses/20200612/CTRL_8C_26psu_1_S17_R1_001_val_1.fq.gz and /gscratch/scrubbed/strigg/analyses/20200612/CTRL_8C_26psu_1_S17_R2_001_val_2.fq.gz (version: v0.22.3)
Bismark was run with Bowtie 2 against the bisulfite genome of /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/ with the specified options: -q --score-min L,0,-0.3 -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:	27136662
Number of paired-end alignments with a unique best hit:	11567049
Mapping efficiency:	42.6% 
Sequence pairs with no alignments under any condition:	10958788
Sequence pairs did not map uniquely:	4610825
Sequence pairs which were discarded because genomic sequence could not be extracted:	2

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	2932114	((converted) top strand)
GA/CT/CT:	2833133	(complementary to (converted) top strand)
GA/CT/GA:	2848876	(complementary to (converted) bottom strand)
CT/GA/GA:	2952924	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	437782672

Total methylated C's in CpG context:	30647578
Total methylated C's in CHG context:	719923
Total methylated C's in CHH context:	3313698
Total methylated C's in Unknown context:	68922

Total unmethylated C's in CpG context:	8885977
Total unmethylated C's in CHG context:	102369915
Total unmethylated C's in CHH context:	291845581
Total unmethylated C's in Unknown context:	354684

C methylated in CpG context:	77.5%
C methylated in CHG context:	0.7%
C methylated in CHH context:	1.1%
C methylated in unknown context (CN or CHN):	16.3%


Bismark completed in 0d 1h 38m 14s