Bismark report for: /gscratch/scrubbed/strigg/TRIMG_adapt_5bp/TRIM_cat/8C_26psu_3_S11_R1_001_val_1.fq.gz and /gscratch/scrubbed/strigg/TRIMG_adapt_5bp/TRIM_cat/8C_26psu_3_S11_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/ 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:	34321341
Number of paired-end alignments with a unique best hit:	17531652
Mapping efficiency:	51.1% 
Sequence pairs with no alignments under any condition:	9675023
Sequence pairs did not map uniquely:	7114666
Sequence pairs which were discarded because genomic sequence could not be extracted:	1782

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	4550197	((converted) top strand)
GA/CT/CT:	4173653	(complementary to (converted) top strand)
GA/CT/GA:	4212730	(complementary to (converted) bottom strand)
CT/GA/GA:	4593290	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	687992764

Total methylated C's in CpG context:	56625818
Total methylated C's in CHG context:	2350349
Total methylated C's in CHH context:	12001180
Total methylated C's in Unknown context:	997880


Total unmethylated C's in CpG context:	16826693
Total unmethylated C's in CHG context:	177447140
Total unmethylated C's in CHH context:	422741584
Total unmethylated C's in Unknown context:	2249618


C methylated in CpG context:	77.1%
C methylated in CHG context:	1.3%
C methylated in CHH context:	2.8%
C methylated in unknown context (CN or CHN):	30.7%


Bismark completed in 0d 3h 51m 26s