Bismark report for: /gscratch/scrubbed/samwhite/data/C_gigas/BSseq/cgig_bsseq_pe_all_R1.fastq.gz and /gscratch/scrubbed/samwhite/data/C_gigas/BSseq/cgig_bsseq_pe_all_R2.fastq.gz (version: v0.19.0)
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 --no-mixed --no-discordant --dovetail --maxins 500
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:	487600
Mapping efficiency:	24.4% 
Sequence pairs with no alignments under any condition:	1365034
Sequence pairs did not map uniquely:	147366
Sequence pairs which were discarded because genomic sequence could not be extracted:	19

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	247986	((converted) top strand)
GA/CT/CT:	0	(complementary to (converted) top strand)
GA/CT/GA:	0	(complementary to (converted) bottom strand)
CT/GA/GA:	239595	((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:	6366907

Total methylated C's in CpG context:	91154
Total methylated C's in CHG context:	3123
Total methylated C's in CHH context:	11232
Total methylated C's in Unknown context:	1069


Total unmethylated C's in CpG context:	661830
Total unmethylated C's in CHG context:	1036674
Total unmethylated C's in CHH context:	4562894
Total unmethylated C's in Unknown context:	10512


C methylated in CpG context:	12.1%
C methylated in CHG context:	0.3%
C methylated in CHH context:	0.2%
C methylated in unknown context (CN or CHN):	9.2%


Bismark completed in 0d 0h 8m 48s