Bismark report for: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/16C_26psu_1_S13_L001_R1_001.fastq.gz and /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/16C_26psu_1_S13_L001_R2_001.fastq.gz (version: v0.19.0)
Bismark was run with Bowtie 2 against the bisulfite genome of /gscratch/srlab/strigg/data/Ssalar/GENOMES/ with the specified options: -q --score-min L,0,-0.6 -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:	22721
Mapping efficiency:	22.7% 
Sequence pairs with no alignments under any condition:	72870
Sequence pairs did not map uniquely:	4409
Sequence pairs which were discarded because genomic sequence could not be extracted:	5

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	5782	((converted) top strand)
GA/CT/CT:	5481	(complementary to (converted) top strand)
GA/CT/GA:	5599	(complementary to (converted) bottom strand)
CT/GA/GA:	5854	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	1331795

Total methylated C's in CpG context:	99771
Total methylated C's in CHG context:	8690
Total methylated C's in CHH context:	25724
Total methylated C's in Unknown context:	5813


Total unmethylated C's in CpG context:	31936
Total unmethylated C's in CHG context:	326811
Total unmethylated C's in CHH context:	838863
Total unmethylated C's in Unknown context:	7810


C methylated in CpG context:	75.8%
C methylated in CHG context:	2.6%
C methylated in CHH context:	3.0%
C methylated in unknown context (CN or CHN):	42.7%


Bismark completed in 0d 0h 1m 43s