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 05:39 on 2019-12-21


Alignment Stats

Sequence pairs analysed in total 16300374
Paired-end alignments with a unique best hit 6871477
Pairs without alignments under any condition 7612342
Pairs that did not map uniquely 1816555
Genomic sequence context not extractable (edges of chromosomes) 2

Cytosine Methylation

Total C's analysed 195629573
Methylated C's in CpG context 8208009
Methylated C's in CHG context 1115053
Methylated C's in CHH context 3356022
Methylated C's in Unknown context 59602
Unmethylated C's in CpG context 19626346
Unmethylated C's in CHG context 41123332
Unmethylated C's in CHH context 122200811
Unmethylated C's in Unknown context 418497
Percentage methylation (CpG context) 29.5%
Percentage methylation (CHG context) 2.6%
Percentage methylation (CHH context) 2.7%
Methylated C's in Unknown context N/A%

Alignment to Individual Bisulfite Strands

OT 3394540 original top strand
CTOT 0 complementary to original top strand
CTOB 0 complementary to original bottom strand
OB 3476935 original bottom strand

Deduplication

Alignments analysed 6871475
Unique alignments 4911622
Duplicates removed 1959853
Duplicated alignments were found at 1245701 different positions

Cytosine Methylation after Extraction

Total C's analysed 96701418
Methylated C's in CpG context 4236787
Methylated C's in CHG context 538030
Methylated C's in CHH context 1814920
Unmethylated C's in CpG context 9099073
Unmethylated C's in CHG context 19735564
Unmethylated C's in CHH context 61277044
Percentage methylation (CpG context) 31.8%
Percentage methylation (CHG context) 2.7%
Percentage methylation (CHH context) 2.9%

M-Bias Plot