Bismark

Bismark Processing Report

/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-160_S7_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-160_S7_L002_R2_001_val_2.fq.gz

Data processed at 05:39 on 2019-12-21


Alignment Stats

Sequence pairs analysed in total 31922572
Paired-end alignments with a unique best hit 12255649
Pairs without alignments under any condition 16675995
Pairs that did not map uniquely 2990928
Genomic sequence context not extractable (edges of chromosomes) 1

Cytosine Methylation

Total C's analysed 356119849
Methylated C's in CpG context 13819770
Methylated C's in CHG context 1872039
Methylated C's in CHH context 4292886
Methylated C's in Unknown context 84309
Unmethylated C's in CpG context 37264731
Unmethylated C's in CHG context 75867945
Unmethylated C's in CHH context 223002478
Unmethylated C's in Unknown context 787408
Percentage methylation (CpG context) 27.1%
Percentage methylation (CHG context) 2.4%
Percentage methylation (CHH context) 1.9%
Methylated C's in Unknown context N/A%

Alignment to Individual Bisulfite Strands

OT 6034016 original top strand
CTOT 0 complementary to original top strand
CTOB 0 complementary to original bottom strand
OB 6221632 original bottom strand

Deduplication

Alignments analysed 12255648
Unique alignments 8992066
Duplicates removed 3263582
Duplicated alignments were found at 1915571 different positions

Cytosine Methylation after Extraction

Total C's analysed 176538868
Methylated C's in CpG context 7344361
Methylated C's in CHG context 912079
Methylated C's in CHH context 2297548
Unmethylated C's in CpG context 16933790
Unmethylated C's in CHG context 36262599
Unmethylated C's in CHH context 112788491
Percentage methylation (CpG context) 30.3%
Percentage methylation (CHG context) 2.5%
Percentage methylation (CHH context) 2.0%

M-Bias Plot