Bismark

Bismark Processing Report

/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-154_S5_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-154_S5_L002_R2_001_val_2.fq.gz

Data processed at 05:17 on 2019-12-21


Alignment Stats

Sequence pairs analysed in total 25226760
Paired-end alignments with a unique best hit 9405544
Pairs without alignments under any condition 13904236
Pairs that did not map uniquely 1916980
Genomic sequence context not extractable (edges of chromosomes) 0

Cytosine Methylation

Total C's analysed 285373397
Methylated C's in CpG context 11306006
Methylated C's in CHG context 1298778
Methylated C's in CHH context 3449101
Methylated C's in Unknown context 62682
Unmethylated C's in CpG context 28242299
Unmethylated C's in CHG context 60128621
Unmethylated C's in CHH context 180948592
Unmethylated C's in Unknown context 625876
Percentage methylation (CpG context) 28.6%
Percentage methylation (CHG context) 2.1%
Percentage methylation (CHH context) 1.9%
Methylated C's in Unknown context N/A%

Alignment to Individual Bisulfite Strands

OT 4637602 original top strand
CTOT 0 complementary to original top strand
CTOB 0 complementary to original bottom strand
OB 4767942 original bottom strand

Deduplication

Alignments analysed 9405544
Unique alignments 6769523
Duplicates removed 2636021
Duplicated alignments were found at 1665648 different positions

Cytosine Methylation after Extraction

Total C's analysed 142831749
Methylated C's in CpG context 5958725
Methylated C's in CHG context 672814
Methylated C's in CHH context 1876297
Unmethylated C's in CpG context 13541358
Unmethylated C's in CHG context 29209282
Unmethylated C's in CHH context 91573273
Percentage methylation (CpG context) 30.6%
Percentage methylation (CHG context) 2.3%
Percentage methylation (CHH context) 2.0%

M-Bias Plot