Bismark report for: /gscratch/scrubbed/strigg/analyses/20200306/Meth14_R1_001_val_1.fq.gz and /gscratch/scrubbed/strigg/analyses/20200306/Meth14_R2_001_val_2.fq.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,-0.6 -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:	10000000
Number of paired-end alignments with a unique best hit:	409029
Mapping efficiency:	4.1% 
Sequence pairs with no alignments under any condition:	9357718
Sequence pairs did not map uniquely:	233253
Sequence pairs which were discarded because genomic sequence could not be extracted:	887

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	98742	((converted) top strand)
GA/CT/CT:	114470	(complementary to (converted) top strand)
GA/CT/GA:	96576	(complementary to (converted) bottom strand)
CT/GA/GA:	98354	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	10076541

Total methylated C's in CpG context:	131463
Total methylated C's in CHG context:	75459
Total methylated C's in CHH context:	1102086
Total methylated C's in Unknown context:	93770

Total unmethylated C's in CpG context:	1296948
Total unmethylated C's in CHG context:	1566639
Total unmethylated C's in CHH context:	5903946
Total unmethylated C's in Unknown context:	59465

C methylated in CpG context:	9.2%
C methylated in CHG context:	4.6%
C methylated in CHH context:	15.7%
C methylated in unknown context (CN or CHN):	61.2%


Bismark completed in 0d 0h 11m 42s