Bismark report for: /gscratch/scrubbed/samwhite/outputs/20190312_cvir_gonad_bismark/cvir_bsseq_all_pe_R1.fastq.gz and /gscratch/scrubbed/samwhite/outputs/20190312_cvir_gonad_bismark/cvir_bsseq_all_pe_R2.fastq.gz (version: v0.19.0)
Bismark was run with Bowtie 2 against the bisulfite genome of /gscratch/srlab/sam/data/C_virginica/genomes/GCF_002022765.2_C_virginica-3.0/ with the specified options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500
Option '--non_directional' specified: alignments to all strands were being performed (OT, OB, CTOT, CTOB)

Final Alignment report
======================
Sequence pairs analysed in total:	137957136
Number of paired-end alignments with a unique best hit:	43202908
Mapping efficiency:	31.3% 
Sequence pairs with no alignments under any condition:	73583711
Sequence pairs did not map uniquely:	21170517
Sequence pairs which were discarded because genomic sequence could not be extracted:	3

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	10889831	((converted) top strand)
GA/CT/CT:	10680012	(complementary to (converted) top strand)
GA/CT/GA:	10709675	(complementary to (converted) bottom strand)
CT/GA/GA:	10923387	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	1164865379

Total methylated C's in CpG context:	122873598
Total methylated C's in CHG context:	5054655
Total methylated C's in CHH context:	18234442
Total methylated C's in Unknown context:	674287


Total unmethylated C's in CpG context:	40470898
Total unmethylated C's in CHG context:	261834434
Total unmethylated C's in CHH context:	716397352
Total unmethylated C's in Unknown context:	3802925


C methylated in CpG context:	75.2%
C methylated in CHG context:	1.9%
C methylated in CHH context:	2.5%
C methylated in unknown context (CN or CHN):	15.1%


Bismark completed in 1d 9h 0m 47s