Bismark

Bismark Processing Report

/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-143_S37_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-143_S37_L005_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 728
Pairs without alignments under any condition 99272
Pairs that did not map uniquely 0
Genomic sequence context not extractable (edges of chromosomes) 0

Cytosine Methylation

Total C's analysed 29662
Methylated C's in CpG context 77
Methylated C's in CHG context 262
Methylated C's in CHH context 84
Methylated C's in Unknown context 4
Unmethylated C's in CpG context 8359
Unmethylated C's in CHG context 8219
Unmethylated C's in CHH context 12661
Unmethylated C's in Unknown context 1
Percentage methylation (CpG context) 0.9%
Percentage methylation (CHG context) 3.1%
Percentage methylation (CHH context) 0.7%
Methylated C's in Unknown context N/A%

Alignment to Individual Bisulfite Strands

OT 480 original top strand
CTOT 0 complementary to original top strand
CTOB 0 complementary to original bottom strand
OB 248 original bottom strand

Deduplication

Alignments analysed 728
Unique alignments 695
Duplicates removed 33
Duplicated alignments were found at 26 different positions

Cytosine Methylation after Extraction

Total C's analysed 19494
Methylated C's in CpG context 52
Methylated C's in CHG context 168
Methylated C's in CHH context 55
Unmethylated C's in CpG context 5481
Unmethylated C's in CHG context 5356
Unmethylated C's in CHH context 8382
Percentage methylation (CpG context) 0.9%
Percentage methylation (CHG context) 3.0%
Percentage methylation (CHH context) 0.7%

M-Bias Plot