Bismark

Bismark Processing Report

/gscratch/srlab/sr320/data/cg/zr3534_8_R1.fastp-trim.20201202.fq.gz and /gscratch/srlab/sr320/data/cg/zr3534_8_R2.fastp-trim.20201202.fq.gz

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


Alignment Stats

Sequence pairs analysed in total 90605411
Paired-end alignments with a unique best hit 56433393
Pairs without alignments under any condition 23113850
Pairs that did not map uniquely 11058168
Genomic sequence context not extractable (edges of chromosomes) 6011

Cytosine Methylation

Total C's analysed 1947268128
Methylated C's in CpG context 25821272
Methylated C's in CHG context 1643168
Methylated C's in CHH context 7125148
Methylated C's in Unknown context 65968
Unmethylated C's in CpG context 222451289
Unmethylated C's in CHG context 337884437
Unmethylated C's in CHH context 1352342814
Unmethylated C's in Unknown context 4853363
Percentage methylation (CpG context) 10.4%
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 14026877 original top strand
CTOT 14220103 complementary to original top strand
CTOB 14186470 complementary to original bottom strand
OB 13993932 original bottom strand

Deduplication

Alignments analysed 56427382
Unique alignments 44548953
Duplicates removed 11878429
Duplicated alignments were found at 9584750 different positions

Cytosine Methylation after Extraction

Total C's analysed 1040603346
Methylated C's in CpG context 13392711
Methylated C's in CHG context 867715
Methylated C's in CHH context 3799441
Unmethylated C's in CpG context 118181335
Unmethylated C's in CHG context 178670030
Unmethylated C's in CHH context 725692114
Percentage methylation (CpG context) 10.2%
Percentage methylation (CHG context) 0.5%
Percentage methylation (CHH context) 0.5%

M-Bias Plot