Bismark report for: /gscratch/scrubbed/sr320/031520-TG-bs/Pact_trim/Meth5_R1_001_val_1.fq.gz and /gscratch/scrubbed/sr320/031520-TG-bs/Pact_trim/Meth5_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:	284116370
Number of paired-end alignments with a unique best hit:	176448073
Mapping efficiency:	62.1% 
Sequence pairs with no alignments under any condition:	74938987
Sequence pairs did not map uniquely:	32729310
Sequence pairs which were discarded because genomic sequence could not be extracted:	1476881

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	41946437	((converted) top strand)
GA/CT/CT:	45593288	(complementary to (converted) top strand)
GA/CT/GA:	45674173	(complementary to (converted) bottom strand)
CT/GA/GA:	41757294	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	8047605825

Total methylated C's in CpG context:	80058040
Total methylated C's in CHG context:	12048677
Total methylated C's in CHH context:	34553198
Total methylated C's in Unknown context:	628388

Total unmethylated C's in CpG context:	1691019586
Total unmethylated C's in CHG context:	1586289138
Total unmethylated C's in CHH context:	4643637186
Total unmethylated C's in Unknown context:	14307844

C methylated in CpG context:	4.5%
C methylated in CHG context:	0.8%
C methylated in CHH context:	0.7%
C methylated in unknown context (CN or CHN):	4.2%


Bismark completed in 1d 3h 28m 50s