Bismark report for: /gscratch/scrubbed/samwhite/2018OALarvae_DNAm_discovery/trimmed_files/EF06-EM01-Larvae_R1_001_val_1.fq.gz and /gscratch/scrubbed/samwhite/2018OALarvae_DNAm_discovery/trimmed_files/EF06-EM01-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 8 --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:	56782240
Number of paired-end alignments with a unique best hit:	19254185
Mapping efficiency:	33.9% 
Sequence pairs with no alignments under any condition:	28725008
Sequence pairs did not map uniquely:	8803047
Sequence pairs which were discarded because genomic sequence could not be extracted:	13

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	4541918	((converted) top strand)
GA/CT/CT:	5077191	(complementary to (converted) top strand)
GA/CT/GA:	5090505	(complementary to (converted) bottom strand)
CT/GA/GA:	4544558	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	666787630

Total methylated C's in CpG context:	17066150
Total methylated C's in CHG context:	1883582
Total methylated C's in CHH context:	9735487
Total methylated C's in Unknown context:	310809

Total unmethylated C's in CpG context:	78528070
Total unmethylated C's in CHG context:	132143484
Total unmethylated C's in CHH context:	427430857
Total unmethylated C's in Unknown context:	2747140

C methylated in CpG context:	17.9%
C methylated in CHG context:	1.4%
C methylated in CHH context:	2.2%
C methylated in unknown context (CN or CHN):	10.2%


Bismark completed in 0d 23h 47m 28s