Bismark

Bismark Processing Report

/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-221_S33_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-221_S33_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 469
Pairs without alignments under any condition 99531
Pairs that did not map uniquely 0
Genomic sequence context not extractable (edges of chromosomes) 0

Cytosine Methylation

Total C's analysed 16654
Methylated C's in CpG context 60
Methylated C's in CHG context 210
Methylated C's in CHH context 68
Methylated C's in Unknown context 0
Unmethylated C's in CpG context 4765
Unmethylated C's in CHG context 4711
Unmethylated C's in CHH context 6840
Unmethylated C's in Unknown context 11
Percentage methylation (CpG context) 1.2%
Percentage methylation (CHG context) 4.3%
Percentage methylation (CHH context) 1.0%
Methylated C's in Unknown context N/A%

Alignment to Individual Bisulfite Strands

OT 305 original top strand
CTOT 0 complementary to original top strand
CTOB 0 complementary to original bottom strand
OB 164 original bottom strand

Deduplication

Alignments analysed 469
Unique alignments 431
Duplicates removed 38
Duplicated alignments were found at 26 different positions

Cytosine Methylation after Extraction

Total C's analysed 9867
Methylated C's in CpG context 36
Methylated C's in CHG context 119
Methylated C's in CHH context 49
Unmethylated C's in CpG context 2818
Unmethylated C's in CHG context 2742
Unmethylated C's in CHH context 4103
Percentage methylation (CpG context) 1.3%
Percentage methylation (CHG context) 4.2%
Percentage methylation (CHH context) 1.2%

M-Bias Plot