Bismark report for: /gscratch/scrubbed/sr320/031320-TG-bs/Meth11_R1_001_val_1.fq.gz and /gscratch/scrubbed/sr320/031320-TG-bs/Meth11_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:	4102893
Mapping efficiency:	41.0% 
Sequence pairs with no alignments under any condition:	4102429
Sequence pairs did not map uniquely:	1794678
Sequence pairs which were discarded because genomic sequence could not be extracted:	83

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	950650	((converted) top strand)
GA/CT/CT:	1100492	(complementary to (converted) top strand)
GA/CT/GA:	1100645	(complementary to (converted) bottom strand)
CT/GA/GA:	951023	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	185208654

Total methylated C's in CpG context:	4030466
Total methylated C's in CHG context:	377528
Total methylated C's in CHH context:	1377006
Total methylated C's in Unknown context:	83134

Total unmethylated C's in CpG context:	27094517
Total unmethylated C's in CHG context:	32748085
Total unmethylated C's in CHH context:	119581052
Total unmethylated C's in Unknown context:	531969

C methylated in CpG context:	12.9%
C methylated in CHG context:	1.1%
C methylated in CHH context:	1.1%
C methylated in unknown context (CN or CHN):	13.5%


Bismark completed in 0d 0h 35m 0s