Bismark report for: /gscratch/scrubbed/sr320/031320-TG-bs/Meth10_R1_001_val_1.fq.gz and /gscratch/scrubbed/sr320/031320-TG-bs/Meth10_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:	3970191
Mapping efficiency:	39.7% 
Sequence pairs with no alignments under any condition:	4247889
Sequence pairs did not map uniquely:	1781920
Sequence pairs which were discarded because genomic sequence could not be extracted:	78

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	933598	((converted) top strand)
GA/CT/CT:	1049803	(complementary to (converted) top strand)
GA/CT/GA:	1053949	(complementary to (converted) bottom strand)
CT/GA/GA:	932763	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	177399257

Total methylated C's in CpG context:	3589196
Total methylated C's in CHG context:	396474
Total methylated C's in CHH context:	1417191
Total methylated C's in Unknown context:	95665

Total unmethylated C's in CpG context:	26190877
Total unmethylated C's in CHG context:	31157189
Total unmethylated C's in CHH context:	114648330
Total unmethylated C's in Unknown context:	532919

C methylated in CpG context:	12.1%
C methylated in CHG context:	1.3%
C methylated in CHH context:	1.2%
C methylated in unknown context (CN or CHN):	15.2%


Bismark completed in 0d 0h 33m 47s