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:	100000
Number of alignments with a unique best hit from the different alignments:	18487
Mapping efficiency:	18.5%
Sequences with no alignments under any condition:	71737
Sequences did not map uniquely:	9776
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:	9334	((converted) top strand)
CT/GA:	9153	((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:	278946

Total methylated C's in CpG context:	29321
Total methylated C's in CHG context:	2414
Total methylated C's in CHH context:	18296
Total methylated C's in Unknown context:	124

Total unmethylated C's in CpG context:	9435
Total unmethylated C's in CHG context:	55484
Total unmethylated C's in CHH context:	163996
Total unmethylated C's in Unknown context:	620

C methylated in CpG context:	75.7%
C methylated in CHG context:	4.2%
C methylated in CHH context:	10.0%
C methylated in Unknown context (CN or CHN):	16.7%


Bismark completed in 0d 0h 0m 35s