Bismark report for: /gscratch/srlab/sr320/data/oil/20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT.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:	20811265
Number of alignments with a unique best hit from the different alignments:	1614710
Mapping efficiency:	7.8%
Sequences with no alignments under any condition:	18190123
Sequences did not map uniquely:	1006432
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:	807395	((converted) top strand)
CT/GA:	807315	((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:	31055287

Total methylated C's in CpG context:	3687058
Total methylated C's in CHG context:	4528705
Total methylated C's in CHH context:	18535716
Total methylated C's in Unknown context:	89242

Total unmethylated C's in CpG context:	629367
Total unmethylated C's in CHG context:	1030792
Total unmethylated C's in CHH context:	2643649
Total unmethylated C's in Unknown context:	50723

C methylated in CpG context:	85.4%
C methylated in CHG context:	81.5%
C methylated in CHH context:	87.5%
C methylated in Unknown context (CN or CHN):	63.8%


Bismark completed in 0d 0h 37m 38s