Bismark

Bismark Processing Report

/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-181_S16_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-181_S16_L003_R2_001_val_2.fq.gz

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


Alignment Stats

Sequence pairs analysed in total 27212918
Paired-end alignments with a unique best hit 10790981
Pairs without alignments under any condition 14282015
Pairs that did not map uniquely 2139922
Genomic sequence context not extractable (edges of chromosomes) 1

Cytosine Methylation

Total C's analysed 336107175
Methylated C's in CpG context 13211112
Methylated C's in CHG context 1652081
Methylated C's in CHH context 3893943
Methylated C's in Unknown context 60101
Unmethylated C's in CpG context 34596724
Unmethylated C's in CHG context 71273976
Unmethylated C's in CHH context 211479339
Unmethylated C's in Unknown context 733272
Percentage methylation (CpG context) 27.6%
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 5313318 original top strand
CTOT 0 complementary to original top strand
CTOB 0 complementary to original bottom strand
OB 5477662 original bottom strand

Deduplication

Alignments analysed 10790980
Unique alignments 8210265
Duplicates removed 2580715
Duplicated alignments were found at 1499838 different positions

Cytosine Methylation after Extraction

Total C's analysed 182131746
Methylated C's in CpG context 7773669
Methylated C's in CHG context 910797
Methylated C's in CHH context 2287864
Unmethylated C's in CpG context 17313389
Unmethylated C's in CHG context 37265101
Unmethylated C's in CHH context 116580926
Percentage methylation (CpG context) 31.0%
Percentage methylation (CHG context) 2.4%
Percentage methylation (CHH context) 1.9%

M-Bias Plot