Bismark report for: /gscratch/scrubbed/samwhite/2018OALarvae_DNAm_discovery/trimmed_files/CF02-CM02-Zygote_R1_001_val_1.fq.gz and /gscratch/scrubbed/samwhite/2018OALarvae_DNAm_discovery/trimmed_files/CF02-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:	67063678
Number of paired-end alignments with a unique best hit:	10105983
Mapping efficiency:	15.1% 
Sequence pairs with no alignments under any condition:	50657462
Sequence pairs did not map uniquely:	6300233
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:	3000851	((converted) top strand)
GA/CT/CT:	2072592	(complementary to (converted) top strand)
GA/CT/GA:	2052690	(complementary to (converted) bottom strand)
CT/GA/GA:	2979844	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	188887969

Total methylated C's in CpG context:	4107683
Total methylated C's in CHG context:	1286993
Total methylated C's in CHH context:	13086957
Total methylated C's in Unknown context:	266487

Total unmethylated C's in CpG context:	16031720
Total unmethylated C's in CHG context:	29129543
Total unmethylated C's in CHH context:	125245073
Total unmethylated C's in Unknown context:	1213471

C methylated in CpG context:	20.4%
C methylated in CHG context:	4.2%
C methylated in CHH context:	9.5%
C methylated in unknown context (CN or CHN):	18.0%


Bismark completed in 0d 14h 42m 49s