Bismark report for: /gscratch/srlab/sr320/data/cg-big/zrtg3616_8_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zrtg3616_8_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:	61458
Mapping efficiency:	61.5% 
Sequence pairs with no alignments under any condition:	18881
Sequence pairs did not map uniquely:	19661
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:	15324	((converted) top strand)
GA/CT/CT:	15381	(complementary to (converted) top strand)
GA/CT/GA:	15359	(complementary to (converted) bottom strand)
CT/GA/GA:	15394	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	2027999

Total methylated C's in CpG context:	30597
Total methylated C's in CHG context:	1889
Total methylated C's in CHH context:	8508
Total methylated C's in Unknown context:	101

Total unmethylated C's in CpG context:	247291
Total unmethylated C's in CHG context:	367521
Total unmethylated C's in CHH context:	1372193
Total unmethylated C's in Unknown context:	4708

C methylated in CpG context:	11.0%
C methylated in CHG context:	0.5%
C methylated in CHH context:	0.6%
C methylated in unknown context (CN or CHN):	2.1%


Bismark completed in 0d 0h 0m 49s