Bismark

Bismark Processing Report

/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-184_S18_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-184_S18_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 457
Pairs without alignments under any condition 99543
Pairs that did not map uniquely 0
Genomic sequence context not extractable (edges of chromosomes) 0

Cytosine Methylation

Total C's analysed 17774
Methylated C's in CpG context 57
Methylated C's in CHG context 191
Methylated C's in CHH context 84
Methylated C's in Unknown context 1
Unmethylated C's in CpG context 4960
Unmethylated C's in CHG context 4864
Unmethylated C's in CHH context 7618
Unmethylated C's in Unknown context 3
Percentage methylation (CpG context) 1.1%
Percentage methylation (CHG context) 3.8%
Percentage methylation (CHH context) 1.1%
Methylated C's in Unknown context N/A%

Alignment to Individual Bisulfite Strands

OT 295 original top strand
CTOT 0 complementary to original top strand
CTOB 0 complementary to original bottom strand
OB 162 original bottom strand

Deduplication

Alignments analysed 457
Unique alignments 430
Duplicates removed 27
Duplicated alignments were found at 20 different positions

Cytosine Methylation after Extraction

Total C's analysed 11172
Methylated C's in CpG context 37
Methylated C's in CHG context 114
Methylated C's in CHH context 57
Unmethylated C's in CpG context 3105
Unmethylated C's in CHG context 3016
Unmethylated C's in CHH context 4843
Percentage methylation (CpG context) 1.2%
Percentage methylation (CHG context) 3.6%
Percentage methylation (CHH context) 1.2%

M-Bias Plot