Bismark

Bismark Processing Report

/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-152_S3_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-152_S3_L002_R2_001_val_2.fq.gz

Data processed at 11:37 on 2019-08-07


Alignment Stats

Sequence pairs analysed in total 29855018
Paired-end alignments with a unique best hit 11727816
Pairs without alignments under any condition 15750735
Pairs that did not map uniquely 2376467
Genomic sequence context not extractable (edges of chromosomes) 0

Cytosine Methylation

Total C's analysed 358780662
Methylated C's in CpG context 14625118
Methylated C's in CHG context 1782524
Methylated C's in CHH context 4106805
Methylated C's in Unknown context 73648
Unmethylated C's in CpG context 34864391
Unmethylated C's in CHG context 74934034
Unmethylated C's in CHH context 228467790
Unmethylated C's in Unknown context 784418
Percentage methylation (CpG context) 29.6%
Percentage methylation (CHG context) 2.3%
Percentage methylation (CHH context) 1.8%
Methylated C's in Unknown context N/A%

Alignment to Individual Bisulfite Strands

OT 5811638 original top strand
CTOT 0 complementary to original top strand
CTOB 0 complementary to original bottom strand
OB 5916178 original bottom strand

Deduplication

Alignments analysed 11727816
Unique alignments 8409770
Duplicates removed 3318046
Duplicated alignments were found at 2042936 different positions

Cytosine Methylation after Extraction

Total C's analysed 181742375
Methylated C's in CpG context 7874020
Methylated C's in CHG context 929405
Methylated C's in CHH context 2251146
Unmethylated C's in CpG context 16740253
Unmethylated C's in CHG context 36920601
Unmethylated C's in CHH context 117026950
Percentage methylation (CpG context) 32.0%
Percentage methylation (CHG context) 2.5%
Percentage methylation (CHH context) 1.9%

M-Bias Plot