Bismark

Bismark Processing Report

/gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_10_s1_R1.fastq.gz and /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_10_s1_R2.fastq.gz

Data processed at 03:44 on 2018-11-07


Alignment Stats

Sequence pairs analysed in total 17717127
Paired-end alignments with a unique best hit 6293704
Pairs without alignments under any condition 9714892
Pairs that did not map uniquely 1708531
Genomic sequence context not extractable (edges of chromosomes) 0

Cytosine Methylation

Total C's analysed 232453732
Methylated C's in CpG context 22151409
Methylated C's in CHG context 1632227
Methylated C's in CHH context 5841216
Methylated C's in Unknown context 707839
Unmethylated C's in CpG context 10405571
Unmethylated C's in CHG context 50198281
Unmethylated C's in CHH context 142225028
Unmethylated C's in Unknown context 2858024
Percentage methylation (CpG context) 68.0%
Percentage methylation (CHG context) 3.1%
Percentage methylation (CHH context) 3.9%
Methylated C's in Unknown context N/A%

Alignment to Individual Bisulfite Strands

OT 1601646 original top strand
CTOT 1537591 complementary to original top strand
CTOB 1548913 complementary to original bottom strand
OB 1605554 original bottom strand

Deduplication

Alignments analysed 6293704
Unique alignments 6098678
Duplicates removed 195026
Duplicated alignments were found at 163458 different positions

Cytosine Methylation after Extraction

Total C's analysed 161979006
Methylated C's in CpG context 15010256
Methylated C's in CHG context 1253545
Methylated C's in CHH context 4613320
Unmethylated C's in CpG context 7412133
Unmethylated C's in CHG context 34551003
Unmethylated C's in CHH context 99138749
Percentage methylation (CpG context) 66.9%
Percentage methylation (CHG context) 3.5%
Percentage methylation (CHH context) 4.4%

M-Bias Plot