Bismark report for: 8C_26psu_2_S10_R1_001_val_1.fq.gz and 8C_26psu_2_S10_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,-0.2 -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:	39831
Mapping efficiency:	39.8% 
Sequence pairs with no alignments under any condition:	42072
Sequence pairs did not map uniquely:	18097
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:	10319	((converted) top strand)
GA/CT/CT:	9563	(complementary to (converted) top strand)
GA/CT/GA:	9433	(complementary to (converted) bottom strand)
CT/GA/GA:	10516	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	1474963

Total methylated C's in CpG context:	112454
Total methylated C's in CHG context:	2337
Total methylated C's in CHH context:	9950
Total methylated C's in Unknown context:	93


Total unmethylated C's in CpG context:	32355
Total unmethylated C's in CHG context:	362797
Total unmethylated C's in CHH context:	955070
Total unmethylated C's in Unknown context:	681


C methylated in CpG context:	77.7%
C methylated in CHG context:	0.6%
C methylated in CHH context:	1.0%
C methylated in unknown context (CN or CHN):	12.0%


Bismark completed in 0d 0h 0m 32s