Bismark

Bismark Processing Report

/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-153_S4_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-153_S4_L002_R2_001_val_2.fq.gz

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


Alignment Stats

Sequence pairs analysed in total 26009397
Paired-end alignments with a unique best hit 10439073
Pairs without alignments under any condition 13324084
Pairs that did not map uniquely 2246240
Genomic sequence context not extractable (edges of chromosomes) 2

Cytosine Methylation

Total C's analysed 313246619
Methylated C's in CpG context 12166335
Methylated C's in CHG context 1553054
Methylated C's in CHH context 3545799
Methylated C's in Unknown context 59307
Unmethylated C's in CpG context 33102077
Unmethylated C's in CHG context 67300222
Unmethylated C's in CHH context 195579132
Unmethylated C's in Unknown context 676779
Percentage methylation (CpG context) 26.9%
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 5162472 original top strand
CTOT 0 complementary to original top strand
CTOB 0 complementary to original bottom strand
OB 5276599 original bottom strand

Deduplication

Alignments analysed 10439071
Unique alignments 6699555
Duplicates removed 3739516
Duplicated alignments were found at 2094280 different positions

Cytosine Methylation after Extraction

Total C's analysed 136016129
Methylated C's in CpG context 5750945
Methylated C's in CHG context 699624
Methylated C's in CHH context 1733351
Unmethylated C's in CpG context 13021245
Unmethylated C's in CHG context 28351144
Unmethylated C's in CHH context 86459820
Percentage methylation (CpG context) 30.6%
Percentage methylation (CHG context) 2.4%
Percentage methylation (CHH context) 2.0%

M-Bias Plot