Bismark

Bismark Processing Report

/gscratch/srlab/sr320/data/cg/zr3644_9_R1.fastp-trim.20201206.fq.gz and /gscratch/srlab/sr320/data/cg/zr3644_9_R2.fastp-trim.20201206.fq.gz

Data processed at 15:03 on 2021-02-23


Alignment Stats

Sequence pairs analysed in total 47320068
Paired-end alignments with a unique best hit 29296232
Pairs without alignments under any condition 11480693
Pairs that did not map uniquely 6543143
Genomic sequence context not extractable (edges of chromosomes) 3326

Cytosine Methylation

Total C's analysed 1014421397
Methylated C's in CpG context 14478751
Methylated C's in CHG context 845611
Methylated C's in CHH context 3647281
Methylated C's in Unknown context 36018
Unmethylated C's in CpG context 115919786
Unmethylated C's in CHG context 177548109
Unmethylated C's in CHH context 701981859
Unmethylated C's in Unknown context 2493631
Percentage methylation (CpG context) 11.1%
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 7352634 original top strand
CTOT 7289661 complementary to original top strand
CTOB 7293297 complementary to original bottom strand
OB 7357314 original bottom strand

Deduplication

Alignments analysed 29292906
Unique alignments 25606232
Duplicates removed 3686674
Duplicated alignments were found at 3206124 different positions

Cytosine Methylation after Extraction

Total C's analysed 581087866
Methylated C's in CpG context 8086032
Methylated C's in CHG context 479498
Methylated C's in CHH context 2089186
Unmethylated C's in CpG context 65981858
Unmethylated C's in CHG context 100761982
Unmethylated C's in CHH context 403689310
Percentage methylation (CpG context) 10.9%
Percentage methylation (CHG context) 0.5%
Percentage methylation (CHH context) 0.5%

M-Bias Plot