Bismark

Bismark Processing Report

/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-42_S39_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-42_S39_L005_R2_001_val_2.fq.gz

Data processed at 20:04 on 2019-08-12


Alignment Stats

Sequence pairs analysed in total 29623269
Paired-end alignments with a unique best hit 13173399
Pairs without alignments under any condition 13088150
Pairs that did not map uniquely 3361720
Genomic sequence context not extractable (edges of chromosomes) 0

Cytosine Methylation

Total C's analysed 371864315
Methylated C's in CpG context 17401813
Methylated C's in CHG context 2029825
Methylated C's in CHH context 4531660
Methylated C's in Unknown context 68790
Unmethylated C's in CpG context 35533244
Unmethylated C's in CHG context 78200824
Unmethylated C's in CHH context 234166949
Unmethylated C's in Unknown context 781521
Percentage methylation (CpG context) 32.9%
Percentage methylation (CHG context) 2.5%
Percentage methylation (CHH context) 1.9%
Methylated C's in Unknown context N/A%

Alignment to Individual Bisulfite Strands

OT 6518218 original top strand
CTOT 0 complementary to original top strand
CTOB 0 complementary to original bottom strand
OB 6655181 original bottom strand

Deduplication

Alignments analysed 13173399
Unique alignments 8576017
Duplicates removed 4597382
Duplicated alignments were found at 2730000 different positions

Cytosine Methylation after Extraction

Total C's analysed 167743909
Methylated C's in CpG context 8085260
Methylated C's in CHG context 910439
Methylated C's in CHH context 2251034
Unmethylated C's in CpG context 15228220
Unmethylated C's in CHG context 34537608
Unmethylated C's in CHH context 106731348
Percentage methylation (CpG context) 34.7%
Percentage methylation (CHG context) 2.6%
Percentage methylation (CHH context) 2.1%

M-Bias Plot