Bismark

Bismark Processing Report

/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-214_S30_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-214_S30_L004_R2_001_val_2.fq.gz

Data processed at 05:18 on 2019-12-21


Alignment Stats

Sequence pairs analysed in total 28660043
Paired-end alignments with a unique best hit 11468074
Pairs without alignments under any condition 14622941
Pairs that did not map uniquely 2569028
Genomic sequence context not extractable (edges of chromosomes) 6

Cytosine Methylation

Total C's analysed 344103876
Methylated C's in CpG context 13048066
Methylated C's in CHG context 1676923
Methylated C's in CHH context 4069143
Methylated C's in Unknown context 63794
Unmethylated C's in CpG context 35864648
Unmethylated C's in CHG context 72383593
Unmethylated C's in CHH context 217061503
Unmethylated C's in Unknown context 751976
Percentage methylation (CpG context) 26.7%
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 5665121 original top strand
CTOT 0 complementary to original top strand
CTOB 0 complementary to original bottom strand
OB 5802947 original bottom strand

Deduplication

Alignments analysed 11468068
Unique alignments 8703878
Duplicates removed 2764190
Duplicated alignments were found at 1689980 different positions

Cytosine Methylation after Extraction

Total C's analysed 181129898
Methylated C's in CpG context 7299763
Methylated C's in CHG context 895027
Methylated C's in CHH context 2311106
Unmethylated C's in CpG context 17951668
Unmethylated C's in CHG context 36965157
Unmethylated C's in CHH context 115707177
Percentage methylation (CpG context) 28.9%
Percentage methylation (CHG context) 2.4%
Percentage methylation (CHH context) 2.0%

M-Bias Plot