Bismark report for: /gscratch/scrubbed/samwhite/2018OALarvae_DNAm_discovery/trimmed_files/CF05-CM02-Larvae_R1_001_val_1.fq.gz and /gscratch/scrubbed/samwhite/2018OALarvae_DNAm_discovery/trimmed_files/CF05-CM02-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:	53936905
Number of paired-end alignments with a unique best hit:	19268727
Mapping efficiency:	35.7% 
Sequence pairs with no alignments under any condition:	24852305
Sequence pairs did not map uniquely:	9815873
Sequence pairs which were discarded because genomic sequence could not be extracted:	14

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	4540889	((converted) top strand)
GA/CT/CT:	5088529	(complementary to (converted) top strand)
GA/CT/GA:	5090569	(complementary to (converted) bottom strand)
CT/GA/GA:	4548726	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	632232949

Total methylated C's in CpG context:	17125121
Total methylated C's in CHG context:	1631911
Total methylated C's in CHH context:	9284949
Total methylated C's in Unknown context:	307839

Total unmethylated C's in CpG context:	76864129
Total unmethylated C's in CHG context:	130104233
Total unmethylated C's in CHH context:	397222606
Total unmethylated C's in Unknown context:	2612278

C methylated in CpG context:	18.2%
C methylated in CHG context:	1.2%
C methylated in CHH context:	2.3%
C methylated in unknown context (CN or CHN):	10.5%


Bismark completed in 0d 22h 17m 26s