Bismark

Bismark Processing Report

../output/01.00-F-Ptuh-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_POC-47-TP2_S13_R1_001.fastq.gz and ../output/01.00-F-Ptuh-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_POC-47-TP2_S13_R2_001.fastq.gz

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

Alignment Stats

Sequence pairs analysed in total 151987190
Paired-end alignments with a unique best hit 90000133
Pairs without alignments under any condition 38018588
Pairs that did not map uniquely 23968469
Genomic sequence context not extractable (edges of chromosomes) 93

Cytosine Methylation

Total C's analysed 3022744266
Methylated C's in CpG context 21446654
Methylated C's in CHG context 15194531
Methylated C's in CHH context 62636135
Methylated C's in Unknown context 7115726
Unmethylated C's in CpG context 516406005
Unmethylated C's in CHG context 602797818
Unmethylated C's in CHH context 1804263123
Unmethylated C's in Unknown context 35351450
Percentage methylation (CpG context) 4.0%
Percentage methylation (CHG context) 2.5%
Percentage methylation (CHH context) 3.4%
Methylated C's in Unknown context N/A%

Alignment to Individual Bisulfite Strands

OT 25028895 original top strand
CTOT 20880873 complementary to original top strand
CTOB 20847563 complementary to original bottom strand
OB 23242709 original bottom strand

Deduplication

Alignments analysed 90000040
Unique alignments 75818581
Duplicates removed 14181459
Duplicated alignments were found at 9345136 different positions

Cytosine Methylation after Extraction

Total C's analysed 1337723287
Methylated C's in CpG context 8299945
Methylated C's in CHG context 4835213
Methylated C's in CHH context 26288436
Unmethylated C's in CpG context 227408459
Unmethylated C's in CHG context 265974904
Unmethylated C's in CHH context 804916330
Percentage methylation (CpG context) 3.5%
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 1909722622 116613941 28.69 30.97 16.376
T 1942177719 116748546 29.18 31.00 16.636
C 1264869508 71613560 19.00 19.02 17.662
G 1539194041 71603867 23.13 19.01 21.496
AC 337423561 20840071 5.13 5.53 16.191
CA 405656913 24943498 6.16 6.62 16.263
TC 382120611 22924241 5.81 6.09 16.669
CT 379393689 22427370 5.77 5.96 16.917
CC 237521520 13853764 3.61 3.68 17.145
CG 226515016 10388885 3.44 2.76 21.804
GC 291924160 13995432 4.44 3.72 20.859
GG 336159004 13850871 5.11 3.68 24.270
AG 452076058 22410051 6.87 5.95 20.173
GA 467421482 22896723 7.10 6.08 20.414
TG 505450359 24954009 7.68 6.63 20.255
GT 420086584 20860801 6.38 5.54 20.138
TT 652963033 42681247 9.92 11.33 15.299
TA 380415926 26188985 5.78 6.95 14.526
AT 463827565 30779082 7.05 8.17 15.070
AA 641652569 42584672 9.75 11.31 15.068

M-Bias Plot