Bismark report for: /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_1_s1_R1.fastq.gz and /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_1_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:	28982766
Number of paired-end alignments with a unique best hit:	4521752
Mapping efficiency:	15.6% 
Sequence pairs with no alignments under any condition:	23239578
Sequence pairs did not map uniquely:	1221436
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:	1135164	((converted) top strand)
GA/CT/CT:	1123470	(complementary to (converted) top strand)
GA/CT/GA:	1130861	(complementary to (converted) bottom strand)
CT/GA/GA:	1132256	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	163653583

Total methylated C's in CpG context:	14475033
Total methylated C's in CHG context:	1101550
Total methylated C's in CHH context:	4900521
Total methylated C's in Unknown context:	581418


Total unmethylated C's in CpG context:	6611427
Total unmethylated C's in CHG context:	33757094
Total unmethylated C's in CHH context:	102807958
Total unmethylated C's in Unknown context:	2347522


C methylated in CpG context:	68.6%
C methylated in CHG context:	3.2%
C methylated in CHH context:	4.5%
C methylated in unknown context (CN or CHN):	19.9%


Bismark completed in 0d 4h 32m 38s