Bismark report for: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth3_R1_001.fastq.gz and /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth3_R2_001.fastq.gz (version: v0.21.0)
Bismark was run with Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/froger/Pact_Genome/ 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:	10000
Number of paired-end alignments with a unique best hit:	1100
Mapping efficiency:	11.0% 
Sequence pairs with no alignments under any condition:	8868
Sequence pairs did not map uniquely:	32
Sequence pairs which were discarded because genomic sequence could not be extracted:	1

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	283	((converted) top strand)
GA/CT/CT:	292	(complementary to (converted) top strand)
GA/CT/GA:	272	(complementary to (converted) bottom strand)
CT/GA/GA:	252	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	64170

Total methylated C's in CpG context:	370
Total methylated C's in CHG context:	112
Total methylated C's in CHH context:	385
Total methylated C's in Unknown context:	14

Total unmethylated C's in CpG context:	9361
Total unmethylated C's in CHG context:	11705
Total unmethylated C's in CHH context:	42237
Total unmethylated C's in Unknown context:	53

C methylated in CpG context:	3.8%
C methylated in CHG context:	0.9%
C methylated in CHH context:	0.9%
C methylated in unknown context (CN or CHN):	20.9%


Bismark completed in 0d 0h 2m 33s