Bismark report for: /gscratch/srlab/sr320/data/olurida-bs/3_TTAGGC_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:	11555321
Number of alignments with a unique best hit from the different alignments:	5090692
Mapping efficiency:	44.1%
Sequences with no alignments under any condition:	1486768
Sequences did not map uniquely:	4977861
Sequences which were discarded because genomic sequence could not be extracted:	4594

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	2552558	((converted) top strand)
CT/GA:	2533540	((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:	27529174

Total methylated C's in CpG context:	1070205
Total methylated C's in CHG context:	62804
Total methylated C's in CHH context:	261548
Total methylated C's in Unknown context:	4043

Total unmethylated C's in CpG context:	3122098
Total unmethylated C's in CHG context:	5441541
Total unmethylated C's in CHH context:	17570978
Total unmethylated C's in Unknown context:	69965

C methylated in CpG context:	25.5%
C methylated in CHG context:	1.1%
C methylated in CHH context:	1.5%
C methylated in Unknown context (CN or CHN):	5.5%


Bismark completed in 0d 0h 16m 45s