Bismark

Bismark Processing Report

../output/01.00-E-Peve-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_POR-82-TP2_S8_R1_001.fastq.gz and ../output/01.00-E-Peve-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_POR-82-TP2_S8_R2_001.fastq.gz

Data processed at 08:21:36 on 2025-05-01

Alignment Stats

Sequence pairs analysed in total 263184807
Paired-end alignments with a unique best hit 133958023
Pairs without alignments under any condition 77559917
Pairs that did not map uniquely 51666867
Genomic sequence context not extractable (edges of chromosomes) 16676

Cytosine Methylation

Total C's analysed 5147095758
Methylated C's in CpG context 69268923
Methylated C's in CHG context 22171600
Methylated C's in CHH context 106225883
Methylated C's in Unknown context 11967910
Unmethylated C's in CpG context 860816453
Unmethylated C's in CHG context 967164747
Unmethylated C's in CHH context 3121448152
Unmethylated C's in Unknown context 59314074
Percentage methylation (CpG context) 7.4%
Percentage methylation (CHG context) 2.2%
Percentage methylation (CHH context) 3.3%
Methylated C's in Unknown context N/A%

Alignment to Individual Bisulfite Strands

OT 35550794 original top strand
CTOT 30874303 complementary to original top strand
CTOB 30597762 complementary to original bottom strand
OB 36918488 original bottom strand

Deduplication

Alignments analysed 133941347
Unique alignments 89335723
Duplicates removed 44605624
Duplicated alignments were found at 26376895 different positions

Cytosine Methylation after Extraction

Total C's analysed 1938975922
Methylated C's in CpG context 24665807
Methylated C's in CHG context 7386930
Methylated C's in CHH context 36739576
Unmethylated C's in CpG context 319850362
Unmethylated C's in CHG context 362421754
Unmethylated C's in CHH context 1187911493
Percentage methylation (CpG context) 7.2%
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 2527636365 171827598 29.52 30.52 14.710
T 2484393053 171532079 29.01 30.46 14.484
C 1667660474 109822870 19.47 19.51 15.185
G 1884046563 109866618 22.00 19.51 17.148
AC 466745711 31579141 5.51 5.61 14.780
CA 535675072 36499708 6.32 6.48 14.676
TC 475202471 32794098 5.61 5.82 14.490
CT 484773168 32992892 5.72 5.86 14.693
CC 331058560 22948860 3.91 4.08 14.426
CG 298695917 17370180 3.52 3.09 17.196
GC 377489641 22490193 4.45 3.99 16.785
GG 414124782 22992004 4.89 4.08 18.012
AG 550192099 33058515 6.49 5.87 16.643
GA 551393749 32859848 6.50 5.84 16.780
TG 596335357 36435058 7.03 6.47 16.367
GT 514615717 31514166 6.07 5.60 16.330
TT 850038238 63053650 10.03 11.20 13.481
TA 539139709 39235256 6.36 6.97 13.741
AT 608601498 43957702 7.18 7.81 13.845
AA 882912293 63217613 10.42 11.23 13.966

M-Bias Plot