Bismark report for: /gscratch/scrubbed/samwhite/2018OALarvae_DNAm_discovery/trimmed_files/EF08-EM04-Larvae_R1_001_val_1.fq.gz and /gscratch/scrubbed/samwhite/2018OALarvae_DNAm_discovery/trimmed_files/EF08-EM04-Larvae_R2_001_val_2.fq.gz (version: v0.21.0)
Bismark was run with Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cvirg-genome/ with the specified options: -q --score-min L,0,-0.6 -p 4 --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:	62743331
Number of paired-end alignments with a unique best hit:	22325576
Mapping efficiency:	35.6% 
Sequence pairs with no alignments under any condition:	27547702
Sequence pairs did not map uniquely:	12870053
Sequence pairs which were discarded because genomic sequence could not be extracted:	21

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	5482249	((converted) top strand)
GA/CT/CT:	5667672	(complementary to (converted) top strand)
GA/CT/GA:	5684768	(complementary to (converted) bottom strand)
CT/GA/GA:	5490866	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	644792517

Total methylated C's in CpG context:	19814115
Total methylated C's in CHG context:	2991493
Total methylated C's in CHH context:	16246243
Total methylated C's in Unknown context:	475752

Total unmethylated C's in CpG context:	76585909
Total unmethylated C's in CHG context:	133823662
Total unmethylated C's in CHH context:	395331095
Total unmethylated C's in Unknown context:	2728318

C methylated in CpG context:	20.6%
C methylated in CHG context:	2.2%
C methylated in CHH context:	3.9%
C methylated in unknown context (CN or CHN):	14.8%


Bismark completed in 0d 3h 36m 50s