Bismark report for: /Volumes/web/seashell/bu-serine-wd/18-04-07/zr2096_2_s1_R1.fastq.gz and /Volumes/web/seashell/bu-serine-wd/18-04-07/zr2096_2_s1_R2.fastq.gz (version: v0.20.0)
Bismark was run with Bowtie 2 against the bisulfite genome of /Volumes/web/metacarcinus/Cvirginica/GENOMES/v300/Bismark_genome/ with the specified options: -q --score-min L,0,-2 --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:	100000
Number of paired-end alignments with a unique best hit:	79272
Mapping efficiency:	79.3% 
Sequence pairs with no alignments under any condition:	526
Sequence pairs did not map uniquely:	20202
Sequence pairs which were discarded because genomic sequence could not be extracted:	0

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	20068	((converted) top strand)
GA/CT/CT:	19703	(complementary to (converted) top strand)
GA/CT/GA:	19524	(complementary to (converted) bottom strand)
CT/GA/GA:	19977	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	2315114

Total methylated C's in CpG context:	191418
Total methylated C's in CHG context:	29517
Total methylated C's in CHH context:	221240
Total methylated C's in Unknown context:	42053


Total unmethylated C's in CpG context:	93502
Total unmethylated C's in CHG context:	441550
Total unmethylated C's in CHH context:	1337887
Total unmethylated C's in Unknown context:	79626


C methylated in CpG context:	67.2%
C methylated in CHG context:	6.3%
C methylated in CHH context:	14.2%
C methylated in unknown context (CN or CHN):	34.6%


Bismark completed in 0d 0h 8m 22s