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,-1 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --minins 60 --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:	100000
Number of paired-end alignments with a unique best hit:	59451
Mapping efficiency:	59.5% 
Sequence pairs with no alignments under any condition:	23988
Sequence pairs did not map uniquely:	16561
Sequence pairs which were discarded because genomic sequence could not be extracted:	14

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	14726	((converted) top strand)
GA/CT/CT:	14877	(complementary to (converted) top strand)
GA/CT/GA:	15105	(complementary to (converted) bottom strand)
CT/GA/GA:	14729	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	2814290

Total methylated C's in CpG context:	198435
Total methylated C's in CHG context:	10514
Total methylated C's in CHH context:	52328
Total methylated C's in Unknown context:	7823


Total unmethylated C's in CpG context:	74973
Total unmethylated C's in CHG context:	669381
Total unmethylated C's in CHH context:	1808659
Total unmethylated C's in Unknown context:	29095


C methylated in CpG context:	72.6%
C methylated in CHG context:	1.5%
C methylated in CHH context:	2.8%
C methylated in unknown context (CN or CHN):	21.2%


Bismark completed in 0d 0h 1m 35s