Bismark

Bismark Processing Report

/gscratch/srlab/sr320/data/cg/zr3534_3_R1.fastp-trim.20201202.fq.gz and /gscratch/srlab/sr320/data/cg/zr3534_3_R2.fastp-trim.20201202.fq.gz

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


Alignment Stats

Sequence pairs analysed in total 78091157
Paired-end alignments with a unique best hit 48201740
Pairs without alignments under any condition 20842605
Pairs that did not map uniquely 9046812
Genomic sequence context not extractable (edges of chromosomes) 5907

Cytosine Methylation

Total C's analysed 1687458901
Methylated C's in CpG context 25965647
Methylated C's in CHG context 1483141
Methylated C's in CHH context 6349411
Methylated C's in Unknown context 61887
Unmethylated C's in CpG context 190847734
Unmethylated C's in CHG context 293267693
Unmethylated C's in CHH context 1169545275
Unmethylated C's in Unknown context 4206961
Percentage methylation (CpG context) 12.0%
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 12087376 original top strand
CTOT 12043365 complementary to original top strand
CTOB 12002567 complementary to original bottom strand
OB 12062525 original bottom strand

Deduplication

Alignments analysed 48195833
Unique alignments 39435952
Duplicates removed 8759881
Duplicated alignments were found at 7279656 different positions

Cytosine Methylation after Extraction

Total C's analysed 968207655
Methylated C's in CpG context 14454056
Methylated C's in CHG context 837645
Methylated C's in CHH context 3609225
Unmethylated C's in CpG context 108728598
Unmethylated C's in CHG context 166427426
Unmethylated C's in CHH context 674150705
Percentage methylation (CpG context) 11.7%
Percentage methylation (CHG context) 0.5%
Percentage methylation (CHH context) 0.5%

M-Bias Plot