Bismark report for: /gscratch/scrubbed/samwhite/2018OALarvae_DNAm_discovery/trimmed_files/CF08-CM03-Zygote_R1_001_val_1.fq.gz and /gscratch/scrubbed/samwhite/2018OALarvae_DNAm_discovery/trimmed_files/CF08-CM03-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:	66096319
Number of paired-end alignments with a unique best hit:	13081605
Mapping efficiency:	19.8% 
Sequence pairs with no alignments under any condition:	45148855
Sequence pairs did not map uniquely:	7865859
Sequence pairs which were discarded because genomic sequence could not be extracted:	5

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	3802759	((converted) top strand)
GA/CT/CT:	2760336	(complementary to (converted) top strand)
GA/CT/GA:	2739636	(complementary to (converted) bottom strand)
CT/GA/GA:	3778869	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	264045006

Total methylated C's in CpG context:	5688845
Total methylated C's in CHG context:	1263257
Total methylated C's in CHH context:	13624378
Total methylated C's in Unknown context:	301984

Total unmethylated C's in CpG context:	23292990
Total unmethylated C's in CHG context:	42350005
Total unmethylated C's in CHH context:	177825531
Total unmethylated C's in Unknown context:	1586693

C methylated in CpG context:	19.6%
C methylated in CHG context:	2.9%
C methylated in CHH context:	7.1%
C methylated in unknown context (CN or CHN):	16.0%


Bismark completed in 0d 2h 31m 28s