Bismark report for: /gscratch/scrubbed/samwhite/data/C_gigas/BSseq/cgig_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_gigas/genomes/ with the specified options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals

Final Alignment report
======================
Sequences analysed in total:	1000000
Number of alignments with a unique best hit from the different alignments:	550855
Mapping efficiency:	55.1%
Sequences with no alignments under any condition:	206739
Sequences did not map uniquely:	242406
Sequences which were discarded because genomic sequence could not be extracted:	13

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	275768	((converted) top strand)
CT/GA:	275074	((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:	4651517

Total methylated C's in CpG context:	183107
Total methylated C's in CHG context:	29107
Total methylated C's in CHH context:	55066
Total methylated C's in Unknown context:	837

Total unmethylated C's in CpG context:	525499
Total unmethylated C's in CHG context:	956115
Total unmethylated C's in CHH context:	2902623
Total unmethylated C's in Unknown context:	7744

C methylated in CpG context:	25.8%
C methylated in CHG context:	3.0%
C methylated in CHH context:	1.9%
C methylated in Unknown context (CN or CHN):	9.8%


Bismark completed in 0d 0h 5m 19s