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:	5000000
Number of alignments with a unique best hit from the different alignments:	2747063
Mapping efficiency:	54.9%
Sequences with no alignments under any condition:	1043852
Sequences did not map uniquely:	1209085
Sequences which were discarded because genomic sequence could not be extracted:	92

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	1373378	((converted) top strand)
CT/GA:	1373593	((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:	23218150

Total methylated C's in CpG context:	924940
Total methylated C's in CHG context:	145279
Total methylated C's in CHH context:	276054
Total methylated C's in Unknown context:	4421

Total unmethylated C's in CpG context:	2629317
Total unmethylated C's in CHG context:	4788146
Total unmethylated C's in CHH context:	14454414
Total unmethylated C's in Unknown context:	38351

C methylated in CpG context:	26.0%
C methylated in CHG context:	2.9%
C methylated in CHH context:	1.9%
C methylated in Unknown context (CN or CHN):	10.3%


Bismark completed in 0d 0h 25m 23s