Bismark report for: /gscratch/srlab/sr320/data/cg-big/timeout/zrtg3644_7_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/timeout/zrtg3644_7_R2.fq.gz (version: v0.22.3)
Bismark was run with Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ 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:	81572749
Number of paired-end alignments with a unique best hit:	49340377
Mapping efficiency:	60.5% 
Sequence pairs with no alignments under any condition:	19347824
Sequence pairs did not map uniquely:	12884548
Sequence pairs which were discarded because genomic sequence could not be extracted:	198

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	12321508	((converted) top strand)
GA/CT/CT:	12320256	(complementary to (converted) top strand)
GA/CT/GA:	12348540	(complementary to (converted) bottom strand)
CT/GA/GA:	12349875	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	1748557586

Total methylated C's in CpG context:	23524583
Total methylated C's in CHG context:	1465330
Total methylated C's in CHH context:	6122809
Total methylated C's in Unknown context:	59500

Total unmethylated C's in CpG context:	200474379
Total unmethylated C's in CHG context:	300747271
Total unmethylated C's in CHH context:	1216223214
Total unmethylated C's in Unknown context:	4334330

C methylated in CpG context:	10.5%
C methylated in CHG context:	0.5%
C methylated in CHH context:	0.5%
C methylated in unknown context (CN or CHN):	1.4%


Bismark completed in 0d 8h 8m 29s