Bismark report for: /gscratch/scrubbed/sr320/031520-TG-bs/Pact_trim/Meth9_R1_001_val_1.fq.gz and /gscratch/scrubbed/sr320/031520-TG-bs/Pact_trim/Meth9_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/Pact_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:	87033711
Number of paired-end alignments with a unique best hit:	28863167
Mapping efficiency:	33.2% 
Sequence pairs with no alignments under any condition:	54666408
Sequence pairs did not map uniquely:	3504136
Sequence pairs which were discarded because genomic sequence could not be extracted:	156254

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	7044665	((converted) top strand)
GA/CT/CT:	7278804	(complementary to (converted) top strand)
GA/CT/GA:	7325794	(complementary to (converted) bottom strand)
CT/GA/GA:	7057650	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	1185366396

Total methylated C's in CpG context:	34429781
Total methylated C's in CHG context:	3309395
Total methylated C's in CHH context:	12648356
Total methylated C's in Unknown context:	827057

Total unmethylated C's in CpG context:	133513261
Total unmethylated C's in CHG context:	216384943
Total unmethylated C's in CHH context:	785080660
Total unmethylated C's in Unknown context:	4659006

C methylated in CpG context:	20.5%
C methylated in CHG context:	1.5%
C methylated in CHH context:	1.6%
C methylated in unknown context (CN or CHN):	15.1%


Bismark completed in 0d 5h 15m 2s