Bismark report for: /gscratch/srlab/sr320/data/cg-big/zrtg3644_16_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zrtg3644_16_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:	100000
Number of paired-end alignments with a unique best hit:	61417
Mapping efficiency:	61.4% 
Sequence pairs with no alignments under any condition:	21411
Sequence pairs did not map uniquely:	17172
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:	15314	((converted) top strand)
GA/CT/CT:	15456	(complementary to (converted) top strand)
GA/CT/GA:	15634	(complementary to (converted) bottom strand)
CT/GA/GA:	15013	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	2145277

Total methylated C's in CpG context:	29412
Total methylated C's in CHG context:	1874
Total methylated C's in CHH context:	7534
Total methylated C's in Unknown context:	72

Total unmethylated C's in CpG context:	251689
Total unmethylated C's in CHG context:	374150
Total unmethylated C's in CHH context:	1480618
Total unmethylated C's in Unknown context:	5061

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 0h 0m 51s