Bismark report for: 16C_26psu_1_S13_R1_001_val_1.fq.gz and 16C_26psu_1_S13_R2_001_val_2.fq.gz (version: v0.19.0)
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,-0.5 -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:	100000
Number of paired-end alignments with a unique best hit:	44923
Mapping efficiency:	44.9% 
Sequence pairs with no alignments under any condition:	36063
Sequence pairs did not map uniquely:	19014
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:	11482	((converted) top strand)
GA/CT/CT:	10878	(complementary to (converted) top strand)
GA/CT/GA:	10978	(complementary to (converted) bottom strand)
CT/GA/GA:	11585	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	1730056

Total methylated C's in CpG context:	130764
Total methylated C's in CHG context:	3750
Total methylated C's in CHH context:	21603
Total methylated C's in Unknown context:	1090


Total unmethylated C's in CpG context:	40925
Total unmethylated C's in CHG context:	425680
Total unmethylated C's in CHH context:	1107334
Total unmethylated C's in Unknown context:	3645


C methylated in CpG context:	76.2%
C methylated in CHG context:	0.9%
C methylated in CHH context:	1.9%
C methylated in unknown context (CN or CHN):	23.0%


Bismark completed in 0d 0h 0m 36s