Bismark report for: ../SRR1258894_2M_1.fastq and ../SRR1258894_2M_2.fastq (version: v0.19.0)
Bismark was run with Bowtie against the bisulfite genome of /pbld/netapp/home/dslee/Refs/lamda/ with the specified options: -q -n 1 -k 2 --best --maxins 500 --chunkmbs 512
Option '--directional' specified (default mode): alignments to complementary strands (CTOT, CTOB) were ignored (i.e. not performed)

Final Alignment report
======================
Sequence pairs analysed in total:	2000000
Number of paired-end alignments with a unique best hit:	4020
Mapping efficiency:	0.2% 
Sequence pairs with no alignments under any condition:	1995980
Sequence pairs did not map uniquely:	0
Sequence pairs which were discarded because genomic sequence could not be extracted:	14

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	2202	((converted) top strand)
GA/CT/CT:	0	(complementary to (converted) top strand)
GA/CT/GA:	0	(complementary to (converted) bottom strand)
CT/GA/GA:	1818	((converted) bottom strand)

Number of alignments to (merely theoretical) complementary strands being rejected in total:	0

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	211690

Total methylated C's in CpG context:	150
Total methylated C's in CHG context:	176
Total methylated C's in CHH context:	337

Total unmethylated C's in CpG context:	54691
Total unmethylated C's in CHG context:	56870
Total unmethylated C's in CHH context:	99466

C methylated in CpG context:	0.3%
C methylated in CHG context:	0.3%
C methylated in CHH context:	0.3%


Bismark completed in 0d 0h 0m 48s