Bismark report for: /gscratch/scrubbed/strigg/analyses/20200422/TG_SE_FASTQS/16C_26psu_4_S16_L002_R1_001_trimmed.fq.gz (version: v0.22.3)
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/strigg/data/Ssalar/GENOMES/chr1-29MT/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals

Final Alignment report
======================
Sequences analysed in total:	17053995
Number of alignments with a unique best hit from the different alignments:	8994207
Mapping efficiency:	52.7%
Sequences with no alignments under any condition:	4092460
Sequences did not map uniquely:	3967328
Sequences which were discarded because genomic sequence could not be extracted:	1

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	2120189	((converted) top strand)
CT/GA:	2123356	((converted) bottom strand)
GA/CT:	2372580	(complementary to (converted) top strand)
GA/GA:	2378081	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	171266072

Total methylated C's in CpG context:	12629378
Total methylated C's in CHG context:	441967
Total methylated C's in CHH context:	3593105
Total methylated C's in Unknown context:	176525

Total unmethylated C's in CpG context:	3969643
Total unmethylated C's in CHG context:	41682252
Total unmethylated C's in CHH context:	108949727
Total unmethylated C's in Unknown context:	644852

C methylated in CpG context:	76.1%
C methylated in CHG context:	1.0%
C methylated in CHH context:	3.2%
C methylated in Unknown context (CN or CHN):	21.5%


Bismark completed in 0d 0h 32m 28s