Bismark report for: /gscratch/scrubbed/samwhite/2018OALarvae_DNAm_discovery/trimmed_files/EF05-EM01-Larvae_R1_001_val_1.fq.gz and /gscratch/scrubbed/samwhite/2018OALarvae_DNAm_discovery/trimmed_files/EF05-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:	39294742
Number of paired-end alignments with a unique best hit:	11922548
Mapping efficiency:	30.3% 
Sequence pairs with no alignments under any condition:	21460435
Sequence pairs did not map uniquely:	5911759
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:	2903527	((converted) top strand)
GA/CT/CT:	3054689	(complementary to (converted) top strand)
GA/CT/GA:	3059526	(complementary to (converted) bottom strand)
CT/GA/GA:	2904803	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	399118445

Total methylated C's in CpG context:	11209649
Total methylated C's in CHG context:	1135547
Total methylated C's in CHH context:	6939128
Total methylated C's in Unknown context:	307446

Total unmethylated C's in CpG context:	48189502
Total unmethylated C's in CHG context:	82581213
Total unmethylated C's in CHH context:	249063406
Total unmethylated C's in Unknown context:	1774410

C methylated in CpG context:	18.9%
C methylated in CHG context:	1.4%
C methylated in CHH context:	2.7%
C methylated in unknown context (CN or CHN):	14.8%


Bismark completed in 0d 14h 38m 45s