Bismark report for: /gscratch/scrubbed/sr320/031520-TG-bs/Mcap_trim/Meth14_R1_001_val_1.fq.gz and /gscratch/scrubbed/sr320/031520-TG-bs/Mcap_trim/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:	69159859
Number of paired-end alignments with a unique best hit:	36472079
Mapping efficiency:	52.7% 
Sequence pairs with no alignments under any condition:	10355216
Sequence pairs did not map uniquely:	22332564
Sequence pairs which were discarded because genomic sequence could not be extracted:	168

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	9986376	((converted) top strand)
GA/CT/CT:	8265281	(complementary to (converted) top strand)
GA/CT/GA:	8242390	(complementary to (converted) bottom strand)
CT/GA/GA:	9977864	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	1719504853

Total methylated C's in CpG context:	23193334
Total methylated C's in CHG context:	2190014
Total methylated C's in CHH context:	6278238
Total methylated C's in Unknown context:	64206

Total unmethylated C's in CpG context:	347752341
Total unmethylated C's in CHG context:	325108689
Total unmethylated C's in CHH context:	1014982237
Total unmethylated C's in Unknown context:	1766897

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):	3.5%


Bismark completed in 0d 6h 18m 18s