Bismark report for: /gscratch/scrubbed/strigg/TRIMG_adapt_5bp/TRIM_cat/8C_32psu_4_S8_R1_001_val_1.fq.gz and /gscratch/scrubbed/strigg/TRIMG_adapt_5bp/TRIM_cat/8C_32psu_4_S8_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:	29264212
Number of paired-end alignments with a unique best hit:	14084982
Mapping efficiency:	48.1% 
Sequence pairs with no alignments under any condition:	10598154
Sequence pairs did not map uniquely:	4581076
Sequence pairs which were discarded because genomic sequence could not be extracted:	1429

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	3506326	((converted) top strand)
GA/CT/CT:	3510550	(complementary to (converted) top strand)
GA/CT/GA:	3536275	(complementary to (converted) bottom strand)
CT/GA/GA:	3530402	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	653044712

Total methylated C's in CpG context:	47026493
Total methylated C's in CHG context:	1940321
Total methylated C's in CHH context:	8179862
Total methylated C's in Unknown context:	980538


Total unmethylated C's in CpG context:	15830901
Total unmethylated C's in CHG context:	157094385
Total unmethylated C's in CHH context:	422972750
Total unmethylated C's in Unknown context:	2443521


C methylated in CpG context:	74.8%
C methylated in CHG context:	1.2%
C methylated in CHH context:	1.9%
C methylated in unknown context (CN or CHN):	28.6%


Bismark completed in 0d 3h 21m 38s