Bismark report for: /gscratch/scrubbed/samwhite/2018OALarvae_DNAm_discovery/trimmed_files/EF02-EM02-Zygote_R1_001_val_1.fq.gz and /gscratch/scrubbed/samwhite/2018OALarvae_DNAm_discovery/trimmed_files/EF02-EM02-Zygote_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:	56944147
Number of paired-end alignments with a unique best hit:	14177297
Mapping efficiency:	24.9% 
Sequence pairs with no alignments under any condition:	33479307
Sequence pairs did not map uniquely:	9287543
Sequence pairs which were discarded because genomic sequence could not be extracted:	18

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	3991436	((converted) top strand)
GA/CT/CT:	3145292	(complementary to (converted) top strand)
GA/CT/GA:	3103611	(complementary to (converted) bottom strand)
CT/GA/GA:	3936940	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	368303412

Total methylated C's in CpG context:	8219994
Total methylated C's in CHG context:	1030273
Total methylated C's in CHH context:	9468397
Total methylated C's in Unknown context:	343493

Total unmethylated C's in CpG context:	43793710
Total unmethylated C's in CHG context:	72295531
Total unmethylated C's in CHH context:	233495507
Total unmethylated C's in Unknown context:	2399471

C methylated in CpG context:	15.8%
C methylated in CHG context:	1.4%
C methylated in CHH context:	3.9%
C methylated in unknown context (CN or CHN):	12.5%


Bismark completed in 0d 2h 30m 25s