Bismark report for: /gscratch/scrubbed/samwhite/2018OALarvae_DNAm_discovery/trimmed_files/EF07-EM03-Larvae_R1_001_val_1.fq.gz and /gscratch/scrubbed/samwhite/2018OALarvae_DNAm_discovery/trimmed_files/EF07-EM03-Larvae_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:	48379049
Number of paired-end alignments with a unique best hit:	15618590
Mapping efficiency:	32.3% 
Sequence pairs with no alignments under any condition:	25139522
Sequence pairs did not map uniquely:	7620937
Sequence pairs which were discarded because genomic sequence could not be extracted:	6

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	3745895	((converted) top strand)
GA/CT/CT:	4059444	(complementary to (converted) top strand)
GA/CT/GA:	4067743	(complementary to (converted) bottom strand)
CT/GA/GA:	3745502	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	516811610

Total methylated C's in CpG context:	13655464
Total methylated C's in CHG context:	1514430
Total methylated C's in CHH context:	8653755
Total methylated C's in Unknown context:	247522

Total unmethylated C's in CpG context:	59306412
Total unmethylated C's in CHG context:	103483679
Total unmethylated C's in CHH context:	330197870
Total unmethylated C's in Unknown context:	2071696

C methylated in CpG context:	18.7%
C methylated in CHG context:	1.4%
C methylated in CHH context:	2.6%
C methylated in unknown context (CN or CHN):	10.7%


Bismark completed in 0d 2h 44m 11s