Bismark

Bismark Processing Report

/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-187_S20_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-187_S20_L003_R2_001_val_2.fq.gz

Data processed at 14:11 on 2019-11-04


Alignment Stats

Sequence pairs analysed in total 100000
Paired-end alignments with a unique best hit 406
Pairs without alignments under any condition 99594
Pairs that did not map uniquely 0
Genomic sequence context not extractable (edges of chromosomes) 0

Cytosine Methylation

Total C's analysed 16344
Methylated C's in CpG context 69
Methylated C's in CHG context 186
Methylated C's in CHH context 69
Methylated C's in Unknown context 2
Unmethylated C's in CpG context 4667
Unmethylated C's in CHG context 4576
Unmethylated C's in CHH context 6777
Unmethylated C's in Unknown context 3
Percentage methylation (CpG context) 1.5%
Percentage methylation (CHG context) 3.9%
Percentage methylation (CHH context) 1.0%
Methylated C's in Unknown context N/A%

Alignment to Individual Bisulfite Strands

OT 292 original top strand
CTOT 0 complementary to original top strand
CTOB 0 complementary to original bottom strand
OB 114 original bottom strand

Deduplication

Alignments analysed 406
Unique alignments 369
Duplicates removed 37
Duplicated alignments were found at 26 different positions

Cytosine Methylation after Extraction

Total C's analysed 9684
Methylated C's in CpG context 41
Methylated C's in CHG context 99
Methylated C's in CHH context 45
Unmethylated C's in CpG context 2765
Unmethylated C's in CHG context 2683
Unmethylated C's in CHH context 4051
Percentage methylation (CpG context) 1.5%
Percentage methylation (CHG context) 3.6%
Percentage methylation (CHH context) 1.1%

M-Bias Plot