Bismark report for: /gscratch/scrubbed/strigg/analyses/20200612/8C_26psu_2_S10_R1_001_val_1.fq.gz and /gscratch/scrubbed/strigg/analyses/20200612/8C_26psu_2_S10_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:	36473118
Number of paired-end alignments with a unique best hit:	15526271
Mapping efficiency:	42.6% 
Sequence pairs with no alignments under any condition:	13952498
Sequence pairs did not map uniquely:	6994349
Sequence pairs which were discarded because genomic sequence could not be extracted:	1

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	4032212	((converted) top strand)
GA/CT/CT:	3691926	(complementary to (converted) top strand)
GA/CT/GA:	3726392	(complementary to (converted) bottom strand)
CT/GA/GA:	4075740	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	577960714

Total methylated C's in CpG context:	43750881
Total methylated C's in CHG context:	989876
Total methylated C's in CHH context:	4730506
Total methylated C's in Unknown context:	101714

Total unmethylated C's in CpG context:	12919516
Total unmethylated C's in CHG context:	142390693
Total unmethylated C's in CHH context:	373179242
Total unmethylated C's in Unknown context:	464631

C methylated in CpG context:	77.2%
C methylated in CHG context:	0.7%
C methylated in CHH context:	1.3%
C methylated in unknown context (CN or CHN):	18.0%


Bismark completed in 0d 2h 10m 0s