Bismark report for: /gscratch/scrubbed/strigg/TRIMG_adapt_5bp/TRIM_cat/16C_32psu_4_S4_R1_001_val_1.fq.gz and /gscratch/scrubbed/strigg/TRIMG_adapt_5bp/TRIM_cat/16C_32psu_4_S4_R2_001_val_2.fq.gz (version: v0.19.0)
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 --no-mixed --no-discordant --dovetail --maxins 500
Option '--non_directional' specified: alignments to all strands were being performed (OT, OB, CTOT, CTOB)

Final Alignment report
======================
Sequence pairs analysed in total:	31260279
Number of paired-end alignments with a unique best hit:	15610585
Mapping efficiency:	49.9% 
Sequence pairs with no alignments under any condition:	12169059
Sequence pairs did not map uniquely:	3480635
Sequence pairs which were discarded because genomic sequence could not be extracted:	6

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	3870650	((converted) top strand)
GA/CT/CT:	3912208	(complementary to (converted) top strand)
GA/CT/GA:	3936829	(complementary to (converted) bottom strand)
CT/GA/GA:	3890892	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	728888259

Total methylated C's in CpG context:	49671021
Total methylated C's in CHG context:	2042809
Total methylated C's in CHH context:	9841929
Total methylated C's in Unknown context:	891833


Total unmethylated C's in CpG context:	16026258
Total unmethylated C's in CHG context:	175116176
Total unmethylated C's in CHH context:	476190066
Total unmethylated C's in Unknown context:	2391780


C methylated in CpG context:	75.6%
C methylated in CHG context:	1.2%
C methylated in CHH context:	2.0%
C methylated in unknown context (CN or CHN):	27.2%


Bismark completed in 0d 3h 22m 5s