Bismark report for: /gscratch/scrubbed/sr320/031320-TG-bs/Meth14_R1_001_val_1.fq.gz and /gscratch/scrubbed/sr320/031320-TG-bs/Meth14_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:	5281203
Mapping efficiency:	52.8% 
Sequence pairs with no alignments under any condition:	1492479
Sequence pairs did not map uniquely:	3226318
Sequence pairs which were discarded because genomic sequence could not be extracted:	28

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	1445480	((converted) top strand)
GA/CT/CT:	1198164	(complementary to (converted) top strand)
GA/CT/GA:	1196249	(complementary to (converted) bottom strand)
CT/GA/GA:	1441282	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	249244513

Total methylated C's in CpG context:	3369105
Total methylated C's in CHG context:	317330
Total methylated C's in CHH context:	910801
Total methylated C's in Unknown context:	8821

Total unmethylated C's in CpG context:	50401388
Total unmethylated C's in CHG context:	47125020
Total unmethylated C's in CHH context:	147120869
Total unmethylated C's in Unknown context:	255281

C methylated in CpG context:	6.3%
C methylated in CHG context:	0.7%
C methylated in CHH context:	0.6%
C methylated in unknown context (CN or CHN):	3.3%


Bismark completed in 0d 0h 41m 57s