Bismark report for: /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_9_s456_trimmed.fq (version: v0.21.0)
Option '--non_directional' specified: alignments to all strands were being performed (OT, OB, CTOT, CTOB)
Bismark was run with Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/olurida-genomes/v081/ with the specified options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals

Final Alignment report
======================
Sequences analysed in total:	77350922
Number of alignments with a unique best hit from the different alignments:	25389646
Mapping efficiency:	32.8%
Sequences with no alignments under any condition:	21586770
Sequences did not map uniquely:	30374506
Sequences which were discarded because genomic sequence could not be extracted:	21762

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	5701971	((converted) top strand)
CT/GA:	5673126	((converted) bottom strand)
GA/CT:	7018609	(complementary to (converted) top strand)
GA/GA:	6974178	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	150881047

Total methylated C's in CpG context:	16742773
Total methylated C's in CHG context:	575469
Total methylated C's in CHH context:	8126479
Total methylated C's in Unknown context:	3311

Total unmethylated C's in CpG context:	4068096
Total unmethylated C's in CHG context:	29027906
Total unmethylated C's in CHH context:	92340324
Total unmethylated C's in Unknown context:	25961

C methylated in CpG context:	80.5%
C methylated in CHG context:	1.9%
C methylated in CHH context:	8.1%
C methylated in Unknown context (CN or CHN):	11.3%


Bismark completed in 0d 1h 44m 50s