Bismark report for: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth12_R1_001.fastq.gz and /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth12_R2_001.fastq.gz (version: v0.21.0)
Bismark was run with Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/froger/Mcap_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:	1347
Mapping efficiency:	13.5% 
Sequence pairs with no alignments under any condition:	8280
Sequence pairs did not map uniquely:	373
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:	321	((converted) top strand)
GA/CT/CT:	357	(complementary to (converted) top strand)
GA/CT/GA:	367	(complementary to (converted) bottom strand)
CT/GA/GA:	302	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	80095

Total methylated C's in CpG context:	1698
Total methylated C's in CHG context:	151
Total methylated C's in CHH context:	604
Total methylated C's in Unknown context:	19

Total unmethylated C's in CpG context:	11401
Total unmethylated C's in CHG context:	14161
Total unmethylated C's in CHH context:	52080
Total unmethylated C's in Unknown context:	54

C methylated in CpG context:	13.0%
C methylated in CHG context:	1.1%
C methylated in CHH context:	1.1%
C methylated in unknown context (CN or CHN):	26.0%


Bismark completed in 0d 0h 0m 25s