Bismark report for: /gscratch/srlab/sr320/data/olurida-bs/5_ACAGTG_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:	12231319
Number of alignments with a unique best hit from the different alignments:	5362176
Mapping efficiency:	43.8%
Sequences with no alignments under any condition:	1580596
Sequences did not map uniquely:	5288547
Sequences which were discarded because genomic sequence could not be extracted:	5099

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	2683369	((converted) top strand)
CT/GA:	2673708	((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:	28880897

Total methylated C's in CpG context:	1107017
Total methylated C's in CHG context:	63558
Total methylated C's in CHH context:	270074
Total methylated C's in Unknown context:	3973

Total unmethylated C's in CpG context:	3245245
Total unmethylated C's in CHG context:	5740229
Total unmethylated C's in CHH context:	18454774
Total unmethylated C's in Unknown context:	73414

C methylated in CpG context:	25.4%
C methylated in CHG context:	1.1%
C methylated in CHH context:	1.4%
C methylated in Unknown context (CN or CHN):	5.1%


Bismark completed in 0d 0h 17m 55s