Bismark report for: /gscratch/scrubbed/samwhite/data/O_lurida/BSseq/olur_bsseq_all_R1.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/sam/data/O_lurida/genomes/Olurida_v081/oly_v081_bismark_genome/ with the specified options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals

Final Alignment report
======================
Sequences analysed in total:	5000000
Number of alignments with a unique best hit from the different alignments:	2715238
Mapping efficiency:	54.3%
Sequences with no alignments under any condition:	915387
Sequences did not map uniquely:	1369375
Sequences which were discarded because genomic sequence could not be extracted:	2005

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	1351525	((converted) top strand)
CT/GA:	1361708	((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:	23890177

Total methylated C's in CpG context:	1220797
Total methylated C's in CHG context:	139846
Total methylated C's in CHH context:	273458
Total methylated C's in Unknown context:	7542

Total unmethylated C's in CpG context:	2796260
Total unmethylated C's in CHG context:	4903686
Total unmethylated C's in CHH context:	14556130
Total unmethylated C's in Unknown context:	88121

C methylated in CpG context:	30.4%
C methylated in CHG context:	2.8%
C methylated in CHH context:	1.8%
C methylated in Unknown context (CN or CHN):	7.9%


Bismark completed in 0d 0h 25m 58s