Bismark report for: 16C_32psu_4_S4_R1_001_val_1.fq.gz and 16C_32psu_4_S4_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,-0.3 -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:	100000
Number of paired-end alignments with a unique best hit:	40669
Mapping efficiency:	40.7% 
Sequence pairs with no alignments under any condition:	45723
Sequence pairs did not map uniquely:	13608
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:	10049	((converted) top strand)
GA/CT/CT:	10236	(complementary to (converted) top strand)
GA/CT/GA:	10104	(complementary to (converted) bottom strand)
CT/GA/GA:	10280	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	1671819

Total methylated C's in CpG context:	115871
Total methylated C's in CHG context:	2870
Total methylated C's in CHH context:	13994
Total methylated C's in Unknown context:	362


Total unmethylated C's in CpG context:	35330
Total unmethylated C's in CHG context:	397248
Total unmethylated C's in CHH context:	1106506
Total unmethylated C's in Unknown context:	1520


C methylated in CpG context:	76.6%
C methylated in CHG context:	0.7%
C methylated in CHH context:	1.2%
C methylated in unknown context (CN or CHN):	19.2%


Bismark completed in 0d 0h 0m 35s