Bismark report for: /gscratch/scrubbed/sr320/031320-TG-bs/Meth16_R1_001_val_1.fq.gz and /gscratch/scrubbed/sr320/031320-TG-bs/Meth16_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/froger/Mcap_Genome/ 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:	10000000
Number of paired-end alignments with a unique best hit:	2432140
Mapping efficiency:	24.3% 
Sequence pairs with no alignments under any condition:	6399595
Sequence pairs did not map uniquely:	1168265
Sequence pairs which were discarded because genomic sequence could not be extracted:	52

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	603496	((converted) top strand)
GA/CT/CT:	614061	(complementary to (converted) top strand)
GA/CT/GA:	612388	(complementary to (converted) bottom strand)
CT/GA/GA:	602143	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	109327196

Total methylated C's in CpG context:	2848838
Total methylated C's in CHG context:	261374
Total methylated C's in CHH context:	987228
Total methylated C's in Unknown context:	82280

Total unmethylated C's in CpG context:	15471933
Total unmethylated C's in CHG context:	19009241
Total unmethylated C's in CHH context:	70748582
Total unmethylated C's in Unknown context:	348986

C methylated in CpG context:	15.5%
C methylated in CHG context:	1.4%
C methylated in CHH context:	1.4%
C methylated in unknown context (CN or CHN):	19.1%


Bismark completed in 0d 0h 24m 24s