Bismark report for: /gscratch/scrubbed/samwhite/2018OALarvae_DNAm_discovery/trimmed_files/CF07-CM02-Zygote_R1_001_val_1.fq.gz and /gscratch/scrubbed/samwhite/2018OALarvae_DNAm_discovery/trimmed_files/CF07-CM02-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 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:	60588756
Number of paired-end alignments with a unique best hit:	7587682
Mapping efficiency:	12.5% 
Sequence pairs with no alignments under any condition:	48271147
Sequence pairs did not map uniquely:	4729927
Sequence pairs which were discarded because genomic sequence could not be extracted:	7

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	2112107	((converted) top strand)
GA/CT/CT:	1728030	(complementary to (converted) top strand)
GA/CT/GA:	1685694	(complementary to (converted) bottom strand)
CT/GA/GA:	2061844	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	176275607

Total methylated C's in CpG context:	3938080
Total methylated C's in CHG context:	607095
Total methylated C's in CHH context:	9685016
Total methylated C's in Unknown context:	289267

Total unmethylated C's in CpG context:	17009743
Total unmethylated C's in CHG context:	30870019
Total unmethylated C's in CHH context:	114165654
Total unmethylated C's in Unknown context:	961142

C methylated in CpG context:	18.8%
C methylated in CHG context:	1.9%
C methylated in CHH context:	7.8%
C methylated in unknown context (CN or CHN):	23.1%


Bismark completed in 0d 12h 25m 45s