Bismark report for: /gscratch/srlab/sr320/data/cg-big/zrtg3616_5_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zrtg3616_5_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:	61682
Mapping efficiency:	61.7% 
Sequence pairs with no alignments under any condition:	18693
Sequence pairs did not map uniquely:	19625
Sequence pairs which were discarded because genomic sequence could not be extracted:	1

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	15603	((converted) top strand)
GA/CT/CT:	15314	(complementary to (converted) top strand)
GA/CT/GA:	15482	(complementary to (converted) bottom strand)
CT/GA/GA:	15282	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	2012509

Total methylated C's in CpG context:	28226
Total methylated C's in CHG context:	1768
Total methylated C's in CHH context:	7979
Total methylated C's in Unknown context:	76

Total unmethylated C's in CpG context:	245141
Total unmethylated C's in CHG context:	362340
Total unmethylated C's in CHH context:	1367055
Total unmethylated C's in Unknown context:	4713

C methylated in CpG context:	10.3%
C methylated in CHG context:	0.5%
C methylated in CHH context:	0.6%
C methylated in unknown context (CN or CHN):	1.6%


Bismark completed in 0d 0h 0m 50s