Bismark report for: /gscratch/scrubbed/sr320/031520-TG-bs/Pact_trim/Meth1_R1_001_val_1.fq.gz and /gscratch/scrubbed/sr320/031520-TG-bs/Pact_trim/Meth1_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:	74424695
Number of paired-end alignments with a unique best hit:	36318677
Mapping efficiency:	48.8% 
Sequence pairs with no alignments under any condition:	34799849
Sequence pairs did not map uniquely:	3306169
Sequence pairs which were discarded because genomic sequence could not be extracted:	149828

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	8474565	((converted) top strand)
GA/CT/CT:	9561246	(complementary to (converted) top strand)
GA/CT/GA:	9620604	(complementary to (converted) bottom strand)
CT/GA/GA:	8512434	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	1538382421

Total methylated C's in CpG context:	7394976
Total methylated C's in CHG context:	3021456
Total methylated C's in CHH context:	11434246
Total methylated C's in Unknown context:	676167

Total unmethylated C's in CpG context:	227923669
Total unmethylated C's in CHG context:	273965285
Total unmethylated C's in CHH context:	1014642789
Total unmethylated C's in Unknown context:	5141199

C methylated in CpG context:	3.1%
C methylated in CHG context:	1.1%
C methylated in CHH context:	1.1%
C methylated in unknown context (CN or CHN):	11.6%


Bismark completed in 0d 6h 11m 17s