Bismark report for: /gscratch/scrubbed/strigg/analyses/20200612/16C_26psu_3_S15_R1_001_val_1.fq.gz and /gscratch/scrubbed/strigg/analyses/20200612/16C_26psu_3_S15_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:	28985030
Number of paired-end alignments with a unique best hit:	11468438
Mapping efficiency:	39.6% 
Sequence pairs with no alignments under any condition:	12457351
Sequence pairs did not map uniquely:	5059241
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:	2761535	((converted) top strand)
GA/CT/CT:	2959301	(complementary to (converted) top strand)
GA/CT/GA:	2971909	(complementary to (converted) bottom strand)
CT/GA/GA:	2775692	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	425687928

Total methylated C's in CpG context:	30038233
Total methylated C's in CHG context:	839231
Total methylated C's in CHH context:	7934705
Total methylated C's in Unknown context:	72863

Total unmethylated C's in CpG context:	8350089
Total unmethylated C's in CHG context:	107681067
Total unmethylated C's in CHH context:	270844603
Total unmethylated C's in Unknown context:	354961

C methylated in CpG context:	78.2%
C methylated in CHG context:	0.8%
C methylated in CHH context:	2.8%
C methylated in unknown context (CN or CHN):	17.0%


Bismark completed in 0d 1h 47m 35s