Bismark report for: /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH07_24_S14_L001_R1_001_val_1.fq.gz and /gscratch/srlab/lhs3/data/DuMOAR/mbdbs-trimmed/4417/CH07_24_S14_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/sc-con-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:	8340
Mapping efficiency:	20.9% 
Sequence pairs with no alignments under any condition:	25093
Sequence pairs did not map uniquely:	6567
Sequence pairs which were discarded because genomic sequence could not be extracted:	1

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	4168	((converted) top strand)
GA/CT/CT:	0	(complementary to (converted) top strand)
GA/CT/GA:	0	(complementary to (converted) bottom strand)
CT/GA/GA:	4171	((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:	275227

Total methylated C's in CpG context:	2517
Total methylated C's in CHG context:	1156
Total methylated C's in CHH context:	34682
Total methylated C's in Unknown context:	562

Total unmethylated C's in CpG context:	28233
Total unmethylated C's in CHG context:	40274
Total unmethylated C's in CHH context:	168365
Total unmethylated C's in Unknown context:	1195

C methylated in CpG context:	8.2%
C methylated in CHG context:	2.8%
C methylated in CHH context:	17.1%
C methylated in unknown context (CN or CHN):	32.0%


Bismark completed in 0d 0h 1m 10s