Bismark report for: /gscratch/scrubbed/samwhite/2018OALarvae_DNAm_discovery/trimmed_files/EF06-EM06-Larvae_R1_001_val_1.fq.gz and /gscratch/scrubbed/samwhite/2018OALarvae_DNAm_discovery/trimmed_files/EF06-EM06-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:	80247899
Number of paired-end alignments with a unique best hit:	21726849
Mapping efficiency:	27.1% 
Sequence pairs with no alignments under any condition:	48022455
Sequence pairs did not map uniquely:	10498595
Sequence pairs which were discarded because genomic sequence could not be extracted:	20

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	5390863	((converted) top strand)
GA/CT/CT:	5508004	(complementary to (converted) top strand)
GA/CT/GA:	5470207	(complementary to (converted) bottom strand)
CT/GA/GA:	5357755	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	540906480

Total methylated C's in CpG context:	14456921
Total methylated C's in CHG context:	3822113
Total methylated C's in CHH context:	21997184
Total methylated C's in Unknown context:	525384

Total unmethylated C's in CpG context:	53245023
Total unmethylated C's in CHG context:	97253683
Total unmethylated C's in CHH context:	350131556
Total unmethylated C's in Unknown context:	3396653

C methylated in CpG context:	21.4%
C methylated in CHG context:	3.8%
C methylated in CHH context:	5.9%
C methylated in unknown context (CN or CHN):	13.4%


Bismark completed in 1d 2h 39m 19s