Bismark report for: /gscratch/scrubbed/strigg/analyses/20200612/8C_32psu_4_S8_R1_001_val_1.fq.gz and /gscratch/scrubbed/strigg/analyses/20200612/8C_32psu_4_S8_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:	29162017
Number of paired-end alignments with a unique best hit:	11254588
Mapping efficiency:	38.6% 
Sequence pairs with no alignments under any condition:	13313520
Sequence pairs did not map uniquely:	4593909
Sequence pairs which were discarded because genomic sequence could not be extracted:	0

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	2826840	((converted) top strand)
GA/CT/CT:	2779722	(complementary to (converted) top strand)
GA/CT/GA:	2801990	(complementary to (converted) bottom strand)
CT/GA/GA:	2846036	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	454276785

Total methylated C's in CpG context:	33372009
Total methylated C's in CHG context:	717954
Total methylated C's in CHH context:	2811980
Total methylated C's in Unknown context:	109227

Total unmethylated C's in CpG context:	10689210
Total unmethylated C's in CHG context:	108381935
Total unmethylated C's in CHH context:	298303697
Total unmethylated C's in Unknown context:	446724

C methylated in CpG context:	75.7%
C methylated in CHG context:	0.7%
C methylated in CHH context:	0.9%
C methylated in unknown context (CN or CHN):	19.6%


Bismark completed in 0d 1h 40m 29s