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:	13795713
Number of paired-end alignments with a unique best hit:	5070163
Mapping efficiency:	36.8% 
Sequence pairs with no alignments under any condition:	6406379
Sequence pairs did not map uniquely:	2319171
Sequence pairs which were discarded because genomic sequence could not be extracted:	0

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	1285757	((converted) top strand)
GA/CT/CT:	1245006	(complementary to (converted) top strand)
GA/CT/GA:	1247818	(complementary to (converted) bottom strand)
CT/GA/GA:	1291582	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	142342778

Total methylated C's in CpG context:	15059429
Total methylated C's in CHG context:	671225
Total methylated C's in CHH context:	2059702
Total methylated C's in Unknown context:	76501


Total unmethylated C's in CpG context:	5460824
Total unmethylated C's in CHG context:	32006667
Total unmethylated C's in CHH context:	87084931
Total unmethylated C's in Unknown context:	435443


C methylated in CpG context:	73.4%
C methylated in CHG context:	2.1%
C methylated in CHH context:	2.3%
C methylated in unknown context (CN or CHN):	14.9%


Bismark completed in 0d 3h 44m 47s