Bismark

Bismark Processing Report

/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-208_S28_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-208_S28_L004_R2_001_val_2.fq.gz

Data processed at 12:47 on 2019-08-08


Alignment Stats

Sequence pairs analysed in total 29146503
Paired-end alignments with a unique best hit 11240949
Pairs without alignments under any condition 14550345
Pairs that did not map uniquely 3355209
Genomic sequence context not extractable (edges of chromosomes) 4

Cytosine Methylation

Total C's analysed 311618922
Methylated C's in CpG context 11403965
Methylated C's in CHG context 1731400
Methylated C's in CHH context 3248557
Methylated C's in Unknown context 54196
Unmethylated C's in CpG context 33743386
Unmethylated C's in CHG context 67489106
Unmethylated C's in CHH context 194002508
Unmethylated C's in Unknown context 680321
Percentage methylation (CpG context) 25.3%
Percentage methylation (CHG context) 2.5%
Percentage methylation (CHH context) 1.6%
Methylated C's in Unknown context N/A%

Alignment to Individual Bisulfite Strands

OT 5552476 original top strand
CTOT 0 complementary to original top strand
CTOB 0 complementary to original bottom strand
OB 5688469 original bottom strand

Deduplication

Alignments analysed 11240945
Unique alignments 8641341
Duplicates removed 2599604
Duplicated alignments were found at 1452536 different positions

Cytosine Methylation after Extraction

Total C's analysed 158634154
Methylated C's in CpG context 6281105
Methylated C's in CHG context 854946
Methylated C's in CHH context 1753269
Unmethylated C's in CpG context 16254051
Unmethylated C's in CHG context 33112776
Unmethylated C's in CHH context 100378007
Percentage methylation (CpG context) 27.9%
Percentage methylation (CHG context) 2.5%
Percentage methylation (CHH context) 1.7%

M-Bias Plot