Bismark

Bismark Processing Report

/gscratch/srlab/sr320/data/cg/zr3534_5_R1.fastp-trim.20201202.fq.gz and /gscratch/srlab/sr320/data/cg/zr3534_5_R2.fastp-trim.20201202.fq.gz

Data processed at 08:32 on 2021-03-03


Alignment Stats

Sequence pairs analysed in total 84046138
Paired-end alignments with a unique best hit 52697723
Pairs without alignments under any condition 21102648
Pairs that did not map uniquely 10245767
Genomic sequence context not extractable (edges of chromosomes) 6162

Cytosine Methylation

Total C's analysed 1829680541
Methylated C's in CpG context 26942242
Methylated C's in CHG context 1595246
Methylated C's in CHH context 6910004
Methylated C's in Unknown context 63871
Unmethylated C's in CpG context 207856338
Unmethylated C's in CHG context 318664024
Unmethylated C's in CHH context 1267712687
Unmethylated C's in Unknown context 4444706
Percentage methylation (CpG context) 11.5%
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 13201516 original top strand
CTOT 13187576 complementary to original top strand
CTOB 13148746 complementary to original bottom strand
OB 13153723 original bottom strand

Deduplication

Alignments analysed 52691561
Unique alignments 42631307
Duplicates removed 10060254
Duplicated alignments were found at 8293421 different positions

Cytosine Methylation after Extraction

Total C's analysed 1011883701
Methylated C's in CpG context 14467262
Methylated C's in CHG context 867806
Methylated C's in CHH context 3772028
Unmethylated C's in CpG context 114149271
Unmethylated C's in CHG context 174285305
Unmethylated C's in CHH context 704342029
Percentage methylation (CpG context) 11.2%
Percentage methylation (CHG context) 0.5%
Percentage methylation (CHH context) 0.5%

M-Bias Plot