Bismark

Bismark Processing Report

../output/01.00-F-Ptuh-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_POC-53-TP2_S15_R1_001.fastq.gz and ../output/01.00-F-Ptuh-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_POC-53-TP2_S15_R2_001.fastq.gz

Data processed at 06:14:03 on 2025-05-01

Alignment Stats

Sequence pairs analysed in total 141417553
Paired-end alignments with a unique best hit 78836445
Pairs without alignments under any condition 42392655
Pairs that did not map uniquely 20188453
Genomic sequence context not extractable (edges of chromosomes) 93

Cytosine Methylation

Total C's analysed 3026230854
Methylated C's in CpG context 22895388
Methylated C's in CHG context 16320787
Methylated C's in CHH context 58134446
Methylated C's in Unknown context 7696769
Unmethylated C's in CpG context 533555765
Unmethylated C's in CHG context 606361912
Unmethylated C's in CHH context 1788962556
Unmethylated C's in Unknown context 36081212
Percentage methylation (CpG context) 4.1%
Percentage methylation (CHG context) 2.6%
Percentage methylation (CHH context) 3.1%
Methylated C's in Unknown context N/A%

Alignment to Individual Bisulfite Strands

OT 22064650 original top strand
CTOT 18425000 complementary to original top strand
CTOB 18416810 complementary to original bottom strand
OB 19929892 original bottom strand

Deduplication

Alignments analysed 78836352
Unique alignments 60999652
Duplicates removed 17836700
Duplicated alignments were found at 11050284 different positions

Cytosine Methylation after Extraction

Total C's analysed 1293043583
Methylated C's in CpG context 8438370
Methylated C's in CHG context 4848892
Methylated C's in CHH context 23601249
Unmethylated C's in CpG context 225630609
Unmethylated C's in CHG context 257708114
Unmethylated C's in CHH context 772816349
Percentage methylation (CpG context) 3.6%
Percentage methylation (CHG context) N/A%
Percentage methylation (CHH context) N/A%

Nucleotide Coverage

Nucleotide Class Counts Sample Counts Genome% in Sample % in Genome fold coverage
A 1578695435 116613941 28.86 30.97 13.538
T 1592146962 116748546 29.11 31.00 13.637
C 1033021138 71613560 18.88 19.02 14.425
G 1266338329 71603867 23.15 19.01 17.685
AC 277018864 20840071 5.11 5.53 13.293
CA 330314506 24943498 6.10 6.62 13.243
TC 311799837 22924241 5.76 6.09 13.601
CT 310127968 22427370 5.72 5.96 13.828
CC 192258713 13853764 3.55 3.68 13.878
CG 189354372 10388885 3.50 2.76 18.227
GC 241259566 13995432 4.45 3.72 17.238
GG 272796135 13850871 5.04 3.68 19.695
AG 371193304 22410051 6.85 5.95 16.564
GA 388741727 22896723 7.18 6.08 16.978
TG 418518644 24954009 7.73 6.63 16.772
GT 346907138 20860801 6.40 5.54 16.630
TT 536768725 42681247 9.91 11.33 12.576
TA 310280219 26188985 5.73 6.95 11.848
AT 380853711 30779082 7.03 8.17 12.374
AA 539077402 42584672 9.95 11.31 12.659

M-Bias Plot