Bismark report for: /gscratch/srlab/sr320/data/oil/20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC.fastq.gz (version: v0.19.0)
Option '--directional' specified (default mode): alignments to complementary strands (CTOT, CTOB) were ignored (i.e. not performed)
Bismark was run with Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cvirg-genome/ with the specified options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals

Final Alignment report
======================
Sequences analysed in total:	31266957
Number of alignments with a unique best hit from the different alignments:	4744536
Mapping efficiency:	15.2%
Sequences with no alignments under any condition:	23775958
Sequences did not map uniquely:	2746463
Sequences which were discarded because genomic sequence could not be extracted:	0

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	2383630	((converted) top strand)
CT/GA:	2360906	((converted) bottom strand)
GA/CT:	0	(complementary to (converted) top strand)
GA/GA:	0	(complementary to (converted) bottom strand)

Number of alignments to (merely theoretical) complementary strands being rejected in total:	0

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	98368212

Total methylated C's in CpG context:	13851042
Total methylated C's in CHG context:	15940213
Total methylated C's in CHH context:	56779026
Total methylated C's in Unknown context:	264963

Total unmethylated C's in CpG context:	1480605
Total unmethylated C's in CHG context:	3375451
Total unmethylated C's in CHH context:	6941875
Total unmethylated C's in Unknown context:	127002

C methylated in CpG context:	90.3%
C methylated in CHG context:	82.5%
C methylated in CHH context:	89.1%
C methylated in Unknown context (CN or CHN):	67.6%


Bismark completed in 0d 1h 24m 3s