Bismark report for: /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_3_s1_R1.fastq.gz and /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_3_s1_R2.fastq.gz (version: v0.19.0)
Bismark was run with Bowtie 2 against the bisulfite genome of /gscratch/srlab/strigg/data/Cvirg/Bismark_genome/ with the specified options: -q --score-min L,0,-1.2 --ignore-quals --no-mixed --no-discordant --dovetail --minins 100 --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:	29892002
Number of paired-end alignments with a unique best hit:	10170153
Mapping efficiency:	34.0% 
Sequence pairs with no alignments under any condition:	16789874
Sequence pairs did not map uniquely:	2931975
Sequence pairs which were discarded because genomic sequence could not be extracted:	1

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	2554767	((converted) top strand)
GA/CT/CT:	2514160	(complementary to (converted) top strand)
GA/CT/GA:	2537491	(complementary to (converted) bottom strand)
CT/GA/GA:	2563734	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	380186993

Total methylated C's in CpG context:	41316176
Total methylated C's in CHG context:	2588230
Total methylated C's in CHH context:	9338662
Total methylated C's in Unknown context:	1160192


Total unmethylated C's in CpG context:	13734426
Total unmethylated C's in CHG context:	82498352
Total unmethylated C's in CHH context:	230711147
Total unmethylated C's in Unknown context:	4951346


C methylated in CpG context:	75.1%
C methylated in CHG context:	3.0%
C methylated in CHH context:	3.9%
C methylated in unknown context (CN or CHN):	19.0%


Bismark completed in 0d 6h 7m 14s