Bismark

Bismark Processing Report

/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-175_S14_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-175_S14_L003_R2_001_val_2.fq.gz

Data processed at 02:53 on 2020-01-03


Alignment Stats

Sequence pairs analysed in total 24654280
Paired-end alignments with a unique best hit 10209530
Pairs without alignments under any condition 12327982
Pairs that did not map uniquely 2116768
Genomic sequence context not extractable (edges of chromosomes) 1

Cytosine Methylation

Total C's analysed 309993582
Methylated C's in CpG context 11855544
Methylated C's in CHG context 1437285
Methylated C's in CHH context 3685251
Methylated C's in Unknown context 57157
Unmethylated C's in CpG context 31961048
Unmethylated C's in CHG context 65204352
Unmethylated C's in CHH context 195850102
Unmethylated C's in Unknown context 677780
Percentage methylation (CpG context) 27.1%
Percentage methylation (CHG context) 2.2%
Percentage methylation (CHH context) 1.8%
Methylated C's in Unknown context N/A%

Alignment to Individual Bisulfite Strands

OT 5041243 original top strand
CTOT 0 complementary to original top strand
CTOB 0 complementary to original bottom strand
OB 5168286 original bottom strand

Deduplication

Alignments analysed 10209529
Unique alignments 7924620
Duplicates removed 2284909
Duplicated alignments were found at 1428268 different positions

Cytosine Methylation after Extraction

Total C's analysed 169230320
Methylated C's in CpG context 6854838
Methylated C's in CHG context 805593
Methylated C's in CHH context 2153742
Unmethylated C's in CpG context 16729782
Unmethylated C's in CHG context 34594121
Unmethylated C's in CHH context 108092244
Percentage methylation (CpG context) 29.1%
Percentage methylation (CHG context) 2.3%
Percentage methylation (CHH context) 2.0%

M-Bias Plot