Bismark report for: /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_18_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-bs/v98/ with the specified options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals

Final Alignment report
======================
Sequences analysed in total:	55048106
Number of alignments with a unique best hit from the different alignments:	18068736
Mapping efficiency:	32.8%
Sequences with no alignments under any condition:	15701339
Sequences did not map uniquely:	21278031
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:	3964570	((converted) top strand)
CT/GA:	3939560	((converted) bottom strand)
GA/CT:	5099608	(complementary to (converted) top strand)
GA/GA:	5064998	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	109172180

Total methylated C's in CpG context:	13950028
Total methylated C's in CHG context:	447236
Total methylated C's in CHH context:	5912338
Total methylated C's in Unknown context:	4134

Total unmethylated C's in CpG context:	2826959
Total unmethylated C's in CHG context:	22196207
Total unmethylated C's in CHH context:	63839412
Total unmethylated C's in Unknown context:	30681

C methylated in CpG context:	83.1%
C methylated in CHG context:	2.0%
C methylated in CHH context:	8.5%
C methylated in Unknown context (CN or CHN):	11.9%


Bismark completed in 0d 1h 12m 53s