Bismark report for: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth5_R1_001.fastq.gz and /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth5_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:	1738
Mapping efficiency:	17.4% 
Sequence pairs with no alignments under any condition:	8217
Sequence pairs did not map uniquely:	45
Sequence pairs which were discarded because genomic sequence could not be extracted:	3

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	437	((converted) top strand)
GA/CT/CT:	451	(complementary to (converted) top strand)
GA/CT/GA:	464	(complementary to (converted) bottom strand)
CT/GA/GA:	383	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	105380

Total methylated C's in CpG context:	1877
Total methylated C's in CHG context:	148
Total methylated C's in CHH context:	295
Total methylated C's in Unknown context:	14

Total unmethylated C's in CpG context:	19700
Total unmethylated C's in CHG context:	19466
Total unmethylated C's in CHH context:	63894
Total unmethylated C's in Unknown context:	43

C methylated in CpG context:	8.7%
C methylated in CHG context:	0.8%
C methylated in CHH context:	0.5%
C methylated in unknown context (CN or CHN):	24.6%


Bismark completed in 0d 0h 2m 34s