Bismark

Bismark Processing Report

/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-208_S28_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-208_S28_L004_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 1086
Pairs without alignments under any condition 98914
Pairs that did not map uniquely 0
Genomic sequence context not extractable (edges of chromosomes) 0

Cytosine Methylation

Total C's analysed 36315
Methylated C's in CpG context 174
Methylated C's in CHG context 481
Methylated C's in CHH context 183
Methylated C's in Unknown context 1
Unmethylated C's in CpG context 10494
Unmethylated C's in CHG context 10189
Unmethylated C's in CHH context 14794
Unmethylated C's in Unknown context 3
Percentage methylation (CpG context) 1.6%
Percentage methylation (CHG context) 4.5%
Percentage methylation (CHH context) 1.2%
Methylated C's in Unknown context N/A%

Alignment to Individual Bisulfite Strands

OT 712 original top strand
CTOT 0 complementary to original top strand
CTOB 0 complementary to original bottom strand
OB 374 original bottom strand

Deduplication

Alignments analysed 1086
Unique alignments 949
Duplicates removed 137
Duplicated alignments were found at 80 different positions

Cytosine Methylation after Extraction

Total C's analysed 19603
Methylated C's in CpG context 90
Methylated C's in CHG context 260
Methylated C's in CHH context 107
Unmethylated C's in CpG context 5645
Unmethylated C's in CHG context 5406
Unmethylated C's in CHH context 8095
Percentage methylation (CpG context) 1.6%
Percentage methylation (CHG context) 4.6%
Percentage methylation (CHH context) 1.3%

M-Bias Plot