Bismark

Bismark Processing Report

/gscratch/srlab/sr320/data/cg/zr3534_10_R1.fastp-trim.20201202.fq.gz and /gscratch/srlab/sr320/data/cg/zr3534_10_R2.fastp-trim.20201202.fq.gz

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


Alignment Stats

Sequence pairs analysed in total 77576026
Paired-end alignments with a unique best hit 48602093
Pairs without alignments under any condition 19298592
Pairs that did not map uniquely 9675341
Genomic sequence context not extractable (edges of chromosomes) 5385

Cytosine Methylation

Total C's analysed 1702743429
Methylated C's in CpG context 22574441
Methylated C's in CHG context 1346432
Methylated C's in CHH context 5774421
Methylated C's in Unknown context 52411
Unmethylated C's in CpG context 199259426
Unmethylated C's in CHG context 300535225
Unmethylated C's in CHH context 1173253484
Unmethylated C's in Unknown context 4171674
Percentage methylation (CpG context) 10.2%
Percentage methylation (CHG context) 0.4%
Percentage methylation (CHH context) 0.5%
Methylated C's in Unknown context N/A%

Alignment to Individual Bisulfite Strands

OT 12157473 original top strand
CTOT 12164131 complementary to original top strand
CTOB 12137855 complementary to original bottom strand
OB 12137249 original bottom strand

Deduplication

Alignments analysed 48596708
Unique alignments 39493884
Duplicates removed 9102824
Duplicated alignments were found at 7507433 different positions

Cytosine Methylation after Extraction

Total C's analysed 944375423
Methylated C's in CpG context 12141084
Methylated C's in CHG context 735626
Methylated C's in CHH context 3178623
Unmethylated C's in CpG context 109564471
Unmethylated C's in CHG context 164759511
Unmethylated C's in CHH context 653996108
Percentage methylation (CpG context) 10.0%
Percentage methylation (CHG context) 0.4%
Percentage methylation (CHH context) 0.5%

M-Bias Plot