Bismark report for: /gscratch/scrubbed/strigg/analyses/20200612/16C_32psu_4_S4_R1_001_val_1.fq.gz and /gscratch/scrubbed/strigg/analyses/20200612/16C_32psu_4_S4_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:	31149160
Number of paired-end alignments with a unique best hit:	12478761
Mapping efficiency:	40.1% 
Sequence pairs with no alignments under any condition:	14474370
Sequence pairs did not map uniquely:	4196029
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:	3115744	((converted) top strand)
GA/CT/CT:	3108867	(complementary to (converted) top strand)
GA/CT/GA:	3123728	(complementary to (converted) bottom strand)
CT/GA/GA:	3130421	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	511816751

Total methylated C's in CpG context:	35947815
Total methylated C's in CHG context:	841181
Total methylated C's in CHH context:	3811598
Total methylated C's in Unknown context:	102039

Total unmethylated C's in CpG context:	10708852
Total unmethylated C's in CHG context:	121444112
Total unmethylated C's in CHH context:	339063193
Total unmethylated C's in Unknown context:	451506

C methylated in CpG context:	77.0%
C methylated in CHG context:	0.7%
C methylated in CHH context:	1.1%
C methylated in unknown context (CN or CHN):	18.4%


Bismark completed in 0d 1h 49m 27s