Bismark report for: /gscratch/srlab/sr320/data/olurida-bs/4_TGACCA_L001_R1_001_trimmed.fq.gz (version: v0.22.3)
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/olurida-bs/genome/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals

Final Alignment report
======================
Sequences analysed in total:	11408856
Number of alignments with a unique best hit from the different alignments:	5032565
Mapping efficiency:	44.1%
Sequences with no alignments under any condition:	1433341
Sequences did not map uniquely:	4942950
Sequences which were discarded because genomic sequence could not be extracted:	4685

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	2517228	((converted) top strand)
CT/GA:	2510652	((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:	26935252

Total methylated C's in CpG context:	1072508
Total methylated C's in CHG context:	49594
Total methylated C's in CHH context:	229961
Total methylated C's in Unknown context:	3738

Total unmethylated C's in CpG context:	2908879
Total unmethylated C's in CHG context:	5301050
Total unmethylated C's in CHH context:	17373260
Total unmethylated C's in Unknown context:	66047

C methylated in CpG context:	26.9%
C methylated in CHG context:	0.9%
C methylated in CHH context:	1.3%
C methylated in Unknown context (CN or CHN):	5.4%


Bismark completed in 0d 0h 16m 17s