Bismark

Bismark Processing Report

/gscratch/srlab/sr320/data/cg-big/zrtg3644_14_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zrtg3644_14_R2.fq.gz

Data processed at 23:10:12 on 2021-06-09


Alignment Stats

Sequence pairs analysed in total 100000
Paired-end alignments with a unique best hit 61819
Pairs without alignments under any condition 22067
Pairs that did not map uniquely 16114
Genomic sequence context not extractable (edges of chromosomes) 1

Cytosine Methylation

Total C's analysed 2175796
Methylated C's in CpG context 32848
Methylated C's in CHG context 1890
Methylated C's in CHH context 7753
Methylated C's in Unknown context 82
Unmethylated C's in CpG context 247090
Unmethylated C's in CHG context 376369
Unmethylated C's in CHH context 1509846
Unmethylated C's in Unknown context 5246
Percentage methylation (CpG context) 11.7%
Percentage methylation (CHG context) 0.5%
Percentage methylation (CHH context) 0.5%
Methylated C's in Unknown context N/A%

Alignment to Individual Bisulfite Strands

OT 15417 original top strand
CTOT 15428 complementary to original top strand
CTOB 15748 complementary to original bottom strand
OB 15225 original bottom strand

Deduplication

Alignments analysed 61818
Unique alignments 57792
Duplicates removed 4026
Duplicated alignments were found at 3759 different positions

Cytosine Methylation after Extraction

Total C's analysed 1394909
Methylated C's in CpG context 20582
Methylated C's in CHG context 1188
Methylated C's in CHH context 4964
Unmethylated C's in CpG context 157518
Unmethylated C's in CHG context 239212
Unmethylated C's in CHH context 971445
Percentage methylation (CpG context) 11.6%
Percentage methylation (CHG context) 0.5%
Percentage methylation (CHH context) 0.5%

M-Bias Plot