Bismark report for: /gscratch/srlab/strigg/data/Ssalar/FASTQS/20200612/16C_26psu_3_S15_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Ssalar/FASTQS/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/2022/ 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:	11459125
Mapping efficiency:	39.5% 
Sequence pairs with no alignments under any condition:	11366010
Sequence pairs did not map uniquely:	6159895
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:	2781835	((converted) top strand)
GA/CT/CT:	2982966	(complementary to (converted) top strand)
GA/CT/GA:	2947439	(complementary to (converted) bottom strand)
CT/GA/GA:	2746885	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	427554162

Total methylated C's in CpG context:	30606235
Total methylated C's in CHG context:	817673
Total methylated C's in CHH context:	7811756
Total methylated C's in Unknown context:	72450

Total unmethylated C's in CpG context:	8121667
Total unmethylated C's in CHG context:	108185552
Total unmethylated C's in CHH context:	272011279
Total unmethylated C's in Unknown context:	338123

C methylated in CpG context:	79.0%
C methylated in CHG context:	0.8%
C methylated in CHH context:	2.8%
C methylated in unknown context (CN or CHN):	17.6%


Bismark completed in 0d 2h 8m 15s