Bismark report for: /gscratch/scrubbed/strigg/analyses/20200612/CTRL_16C_26psu_2_S21_R1_001_val_1.fq.gz and /gscratch/scrubbed/strigg/analyses/20200612/CTRL_16C_26psu_2_S21_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:	26574551
Number of paired-end alignments with a unique best hit:	9879876
Mapping efficiency:	37.2% 
Sequence pairs with no alignments under any condition:	11156490
Sequence pairs did not map uniquely:	5538185
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:	2640640	((converted) top strand)
GA/CT/CT:	2271291	(complementary to (converted) top strand)
GA/CT/GA:	2297009	(complementary to (converted) bottom strand)
CT/GA/GA:	2670934	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	338084645

Total methylated C's in CpG context:	30235769
Total methylated C's in CHG context:	746460
Total methylated C's in CHH context:	3093410
Total methylated C's in Unknown context:	97271

Total unmethylated C's in CpG context:	8154570
Total unmethylated C's in CHG context:	86382856
Total unmethylated C's in CHH context:	209471580
Total unmethylated C's in Unknown context:	341339

C methylated in CpG context:	78.8%
C methylated in CHG context:	0.9%
C methylated in CHH context:	1.5%
C methylated in unknown context (CN or CHN):	22.2%


Bismark completed in 0d 1h 21m 59s