Bismark report for: /gscratch/scrubbed/samwhite/2018OALarvae_DNAm_discovery/trimmed_files/EF05-EM05-Zygote_R1_001_val_1.fq.gz and /gscratch/scrubbed/samwhite/2018OALarvae_DNAm_discovery/trimmed_files/EF05-EM05-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:	48548054
Number of paired-end alignments with a unique best hit:	4410419
Mapping efficiency:	9.1% 
Sequence pairs with no alignments under any condition:	40594655
Sequence pairs did not map uniquely:	3542980
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:	1139379	((converted) top strand)
GA/CT/CT:	1074108	(complementary to (converted) top strand)
GA/CT/GA:	1066348	(complementary to (converted) bottom strand)
CT/GA/GA:	1130577	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	76674394

Total methylated C's in CpG context:	1156945
Total methylated C's in CHG context:	231352
Total methylated C's in CHH context:	4537735
Total methylated C's in Unknown context:	138959

Total unmethylated C's in CpG context:	7723284
Total unmethylated C's in CHG context:	12186707
Total unmethylated C's in CHH context:	50838371
Total unmethylated C's in Unknown context:	731315

C methylated in CpG context:	13.0%
C methylated in CHG context:	1.9%
C methylated in CHH context:	8.2%
C methylated in unknown context (CN or CHN):	16.0%


Bismark completed in 0d 8h 16m 19s