Bismark report for: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth9_R1_001.fastq.gz and /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth9_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:	507
Mapping efficiency:	5.1% 
Sequence pairs with no alignments under any condition:	9480
Sequence pairs did not map uniquely:	13
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:	122	((converted) top strand)
GA/CT/CT:	140	(complementary to (converted) top strand)
GA/CT/GA:	113	(complementary to (converted) bottom strand)
CT/GA/GA:	132	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	29979

Total methylated C's in CpG context:	712
Total methylated C's in CHG context:	66
Total methylated C's in CHH context:	284
Total methylated C's in Unknown context:	6

Total unmethylated C's in CpG context:	3249
Total unmethylated C's in CHG context:	5490
Total unmethylated C's in CHH context:	20178
Total unmethylated C's in Unknown context:	41

C methylated in CpG context:	18.0%
C methylated in CHG context:	1.2%
C methylated in CHH context:	1.4%
C methylated in unknown context (CN or CHN):	12.8%


Bismark completed in 0d 0h 2m 33s