Bismark report for: /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4416/CH03_04_S5_L001_R1_001_val_1.fq.gz and /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4416/CH03_04_S5_L001_R2_001_val_2.fq.gz (version: v0.21.0)
Bismark was run with Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/dumoar/scaff-genome/ with the specified options: -q --score-min L,0,-0.6 -p 40 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500
Option '--directional' specified (default mode): alignments to complementary strands (CTOT, CTOB) were ignored (i.e. not performed)

Final Alignment report
======================
Sequence pairs analysed in total:	40000
Number of paired-end alignments with a unique best hit:	8490
Mapping efficiency:	21.2% 
Sequence pairs with no alignments under any condition:	22932
Sequence pairs did not map uniquely:	8578
Sequence pairs which were discarded because genomic sequence could not be extracted:	0

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	4274	((converted) top strand)
GA/CT/CT:	0	(complementary to (converted) top strand)
GA/CT/GA:	0	(complementary to (converted) bottom strand)
CT/GA/GA:	4216	((converted) bottom strand)

Number of alignments to (merely theoretical) complementary strands being rejected in total:	0

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	205762

Total methylated C's in CpG context:	2904
Total methylated C's in CHG context:	1192
Total methylated C's in CHH context:	69174
Total methylated C's in Unknown context:	663

Total unmethylated C's in CpG context:	20728
Total unmethylated C's in CHG context:	26444
Total unmethylated C's in CHH context:	85320
Total unmethylated C's in Unknown context:	742

C methylated in CpG context:	12.3%
C methylated in CHG context:	4.3%
C methylated in CHH context:	44.8%
C methylated in unknown context (CN or CHN):	47.2%


Bismark completed in 0d 0h 0m 57s