Bismark

Bismark Processing Report

/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-200_S25_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-200_S25_L003_R2_001_val_2.fq.gz

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


Alignment Stats

Sequence pairs analysed in total 25100695
Paired-end alignments with a unique best hit 10396122
Pairs without alignments under any condition 11933311
Pairs that did not map uniquely 2771262
Genomic sequence context not extractable (edges of chromosomes) 1

Cytosine Methylation

Total C's analysed 292335065
Methylated C's in CpG context 12585999
Methylated C's in CHG context 1652750
Methylated C's in CHH context 4231978
Methylated C's in Unknown context 79283
Unmethylated C's in CpG context 28671686
Unmethylated C's in CHG context 61623093
Unmethylated C's in CHH context 183569559
Unmethylated C's in Unknown context 639910
Percentage methylation (CpG context) 30.5%
Percentage methylation (CHG context) 2.6%
Percentage methylation (CHH context) 2.3%
Methylated C's in Unknown context N/A%

Alignment to Individual Bisulfite Strands

OT 5128955 original top strand
CTOT 0 complementary to original top strand
CTOB 0 complementary to original bottom strand
OB 5267166 original bottom strand

Deduplication

Alignments analysed 10396121
Unique alignments 7500987
Duplicates removed 2895134
Duplicated alignments were found at 1778247 different positions

Cytosine Methylation after Extraction

Total C's analysed 143389134
Methylated C's in CpG context 6473128
Methylated C's in CHG context 794893
Methylated C's in CHH context 2249885
Unmethylated C's in CpG context 13251440
Unmethylated C's in CHG context 29375321
Unmethylated C's in CHH context 91244467
Percentage methylation (CpG context) 32.8%
Percentage methylation (CHG context) 2.6%
Percentage methylation (CHH context) 2.4%

M-Bias Plot