Bismark report for: /gscratch/scrubbed/samwhite/2018OALarvae_DNAm_discovery/trimmed_files/EF07-EM01-Zygote_R1_001_val_1.fq.gz and /gscratch/scrubbed/samwhite/2018OALarvae_DNAm_discovery/trimmed_files/EF07-EM01-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:	75480641
Number of paired-end alignments with a unique best hit:	8248837
Mapping efficiency:	10.9% 
Sequence pairs with no alignments under any condition:	61730915
Sequence pairs did not map uniquely:	5500889
Sequence pairs which were discarded because genomic sequence could not be extracted:	9

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	2410845	((converted) top strand)
GA/CT/CT:	1743331	(complementary to (converted) top strand)
GA/CT/GA:	1725475	(complementary to (converted) bottom strand)
CT/GA/GA:	2369177	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	171219488

Total methylated C's in CpG context:	3194441
Total methylated C's in CHG context:	407198
Total methylated C's in CHH context:	8271861
Total methylated C's in Unknown context:	242482

Total unmethylated C's in CpG context:	16796262
Total unmethylated C's in CHG context:	28691213
Total unmethylated C's in CHH context:	113858513
Total unmethylated C's in Unknown context:	978439

C methylated in CpG context:	16.0%
C methylated in CHG context:	1.4%
C methylated in CHH context:	6.8%
C methylated in unknown context (CN or CHN):	19.9%


Bismark completed in 0d 2h 22m 45s