Bismark report for: /gscratch/scrubbed/strigg/TRIMG_adapt_5bp/TRIM_cat/8C_26psu_2_S10_R1_001_val_1.fq.gz and /gscratch/scrubbed/strigg/TRIMG_adapt_5bp/TRIM_cat/8C_26psu_2_S10_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:	36787094
Number of paired-end alignments with a unique best hit:	19498570
Mapping efficiency:	53.0% 
Sequence pairs with no alignments under any condition:	11691438
Sequence pairs did not map uniquely:	5597086
Sequence pairs which were discarded because genomic sequence could not be extracted:	8

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	5043795	((converted) top strand)
GA/CT/CT:	4654368	(complementary to (converted) top strand)
GA/CT/GA:	4698213	(complementary to (converted) bottom strand)
CT/GA/GA:	5102186	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	831491545

Total methylated C's in CpG context:	61329201
Total methylated C's in CHG context:	2478916
Total methylated C's in CHH context:	12117680
Total methylated C's in Unknown context:	972277


Total unmethylated C's in CpG context:	19501607
Total unmethylated C's in CHG context:	207471905
Total unmethylated C's in CHH context:	528592236
Total unmethylated C's in Unknown context:	2509800


C methylated in CpG context:	75.9%
C methylated in CHG context:	1.2%
C methylated in CHH context:	2.2%
C methylated in unknown context (CN or CHN):	27.9%


Bismark completed in 0d 3h 55m 24s