Bismark report for: /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-120_S32_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-120_S32_L005_R2_001_val_2.fq.gz (version: v0.19.0)
Bismark was run with Bowtie 2 against the bisulfite genome of /gscratch/srlab/strigg/data/Pgenr/ with the specified options: -q --score-min L,0,-1.2 --ignore-quals --no-mixed --no-discordant --dovetail --minins 60 --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:	24140505
Number of paired-end alignments with a unique best hit:	15887911
Mapping efficiency:	65.8% 
Sequence pairs with no alignments under any condition:	3955980
Sequence pairs did not map uniquely:	4296614
Sequence pairs which were discarded because genomic sequence could not be extracted:	54868

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	7495995	((converted) top strand)
GA/CT/CT:	369379	(complementary to (converted) top strand)
GA/CT/GA:	376460	(complementary to (converted) bottom strand)
CT/GA/GA:	7591209	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	506804444

Total methylated C's in CpG context:	14796422
Total methylated C's in CHG context:	2552556
Total methylated C's in CHH context:	17168742
Total methylated C's in Unknown context:	579759


Total unmethylated C's in CpG context:	54673696
Total unmethylated C's in CHG context:	101768912
Total unmethylated C's in CHH context:	315844116
Total unmethylated C's in Unknown context:	2606687


C methylated in CpG context:	21.3%
C methylated in CHG context:	2.4%
C methylated in CHH context:	5.2%
C methylated in unknown context (CN or CHN):	18.2%


Bismark completed in 0d 7h 48m 42s