Bismark

Bismark Processing Report

/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-193_S22_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-193_S22_L003_R2_001_val_2.fq.gz

Data processed at 08:15 on 2019-08-08


Alignment Stats

Sequence pairs analysed in total 26770469
Paired-end alignments with a unique best hit 10697352
Pairs without alignments under any condition 13242455
Pairs that did not map uniquely 2830662
Genomic sequence context not extractable (edges of chromosomes) 0

Cytosine Methylation

Total C's analysed 301211333
Methylated C's in CpG context 12254387
Methylated C's in CHG context 1506836
Methylated C's in CHH context 3959201
Methylated C's in Unknown context 62246
Unmethylated C's in CpG context 30734018
Unmethylated C's in CHG context 63666955
Unmethylated C's in CHH context 189089936
Unmethylated C's in Unknown context 644527
Percentage methylation (CpG context) 28.5%
Percentage methylation (CHG context) 2.3%
Percentage methylation (CHH context) 2.1%
Methylated C's in Unknown context N/A%

Alignment to Individual Bisulfite Strands

OT 5278754 original top strand
CTOT 0 complementary to original top strand
CTOB 0 complementary to original bottom strand
OB 5418598 original bottom strand

Deduplication

Alignments analysed 10697352
Unique alignments 8170923
Duplicates removed 2526429
Duplicated alignments were found at 1585629 different positions

Cytosine Methylation after Extraction

Total C's analysed 156322050
Methylated C's in CpG context 6612365
Methylated C's in CHG context 770831
Methylated C's in CHH context 2168983
Unmethylated C's in CpG context 15198462
Unmethylated C's in CHG context 31981857
Unmethylated C's in CHH context 99589552
Percentage methylation (CpG context) 30.3%
Percentage methylation (CHG context) 2.4%
Percentage methylation (CHH context) 2.1%

M-Bias Plot