Bismark report for: /gscratch/scrubbed/samwhite/data/C_virginica/BSseq/cvir_bsseq_all_R1.fastq.gz (version: v0.19.0)
Option '--directional' specified (default mode): alignments to complementary strands (CTOT, CTOB) were ignored (i.e. not performed)
Bismark was run with Bowtie 2 against the bisulfite genome of /gscratch/srlab/sam/data/C_virginica/genomes/ with the specified options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals

Final Alignment report
======================
Sequences analysed in total:	5000000
Number of alignments with a unique best hit from the different alignments:	932056
Mapping efficiency:	18.6%
Sequences with no alignments under any condition:	3569125
Sequences did not map uniquely:	498819
Sequences which were discarded because genomic sequence could not be extracted:	0

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	465565	((converted) top strand)
CT/GA:	466491	((converted) bottom strand)
GA/CT:	0	(complementary to (converted) top strand)
GA/GA:	0	(complementary to (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:	13856975

Total methylated C's in CpG context:	1398936
Total methylated C's in CHG context:	104800
Total methylated C's in CHH context:	830345
Total methylated C's in Unknown context:	5744

Total unmethylated C's in CpG context:	543601
Total unmethylated C's in CHG context:	2810688
Total unmethylated C's in CHH context:	8168605
Total unmethylated C's in Unknown context:	31261

C methylated in CpG context:	72.0%
C methylated in CHG context:	3.6%
C methylated in CHH context:	9.2%
C methylated in Unknown context (CN or CHN):	15.5%


Bismark completed in 0d 0h 12m 47s