Bismark

Bismark Processing Report

/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-199_S24_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-199_S24_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 488
Pairs without alignments under any condition 99512
Pairs that did not map uniquely 0
Genomic sequence context not extractable (edges of chromosomes) 0

Cytosine Methylation

Total C's analysed 17466
Methylated C's in CpG context 65
Methylated C's in CHG context 190
Methylated C's in CHH context 74
Methylated C's in Unknown context 4
Unmethylated C's in CpG context 4904
Unmethylated C's in CHG context 4687
Unmethylated C's in CHH context 7546
Unmethylated C's in Unknown context 5
Percentage methylation (CpG context) 1.3%
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 323 original top strand
CTOT 0 complementary to original top strand
CTOB 0 complementary to original bottom strand
OB 165 original bottom strand

Deduplication

Alignments analysed 488
Unique alignments 419
Duplicates removed 69
Duplicated alignments were found at 42 different positions

Cytosine Methylation after Extraction

Total C's analysed 9683
Methylated C's in CpG context 35
Methylated C's in CHG context 106
Methylated C's in CHH context 44
Unmethylated C's in CpG context 2658
Unmethylated C's in CHG context 2560
Unmethylated C's in CHH context 4280
Percentage methylation (CpG context) 1.3%
Percentage methylation (CHG context) 4.0%
Percentage methylation (CHH context) 1.0%

M-Bias Plot