Bismark report for: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth14_R1_001.fastq.gz and /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth14_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_02/ 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:	2134
Mapping efficiency:	21.3% 
Sequence pairs with no alignments under any condition:	7604
Sequence pairs did not map uniquely:	262
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:	563	((converted) top strand)
GA/CT/CT:	508	(complementary to (converted) top strand)
GA/CT/GA:	502	(complementary to (converted) bottom strand)
CT/GA/GA:	561	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	129470

Total methylated C's in CpG context:	3274
Total methylated C's in CHG context:	208
Total methylated C's in CHH context:	555
Total methylated C's in Unknown context:	22

Total unmethylated C's in CpG context:	25305
Total unmethylated C's in CHG context:	22226
Total unmethylated C's in CHH context:	77902
Total unmethylated C's in Unknown context:	80

C methylated in CpG context:	11.5%
C methylated in CHG context:	0.9%
C methylated in CHH context:	0.7%
C methylated in unknown context (CN or CHN):	21.6%


Bismark completed in 0d 0h 0m 26s