Bismark report for: /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_10_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/v082/ with the specified options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals

Final Alignment report
======================
Sequences analysed in total:	78221457
Number of alignments with a unique best hit from the different alignments:	3147226
Mapping efficiency:	4.0%
Sequences with no alignments under any condition:	71822548
Sequences did not map uniquely:	3251683
Sequences which were discarded because genomic sequence could not be extracted:	75

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	763339	((converted) top strand)
CT/GA:	808464	((converted) bottom strand)
GA/CT:	766511	(complementary to (converted) top strand)
GA/GA:	808837	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	19635772

Total methylated C's in CpG context:	2906053
Total methylated C's in CHG context:	106168
Total methylated C's in CHH context:	1071747
Total methylated C's in Unknown context:	120

Total unmethylated C's in CpG context:	877521
Total unmethylated C's in CHG context:	3583731
Total unmethylated C's in CHH context:	11090552
Total unmethylated C's in Unknown context:	424

C methylated in CpG context:	76.8%
C methylated in CHG context:	2.9%
C methylated in CHH context:	8.8%
C methylated in Unknown context (CN or CHN):	22.1%


Bismark completed in 0d 0h 38m 54s