Bismark

Bismark Processing Report

../output/01.00-E-Peve-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_POR-79-TP2_S10_R1_001.fastq.gz and ../output/01.00-E-Peve-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_POR-79-TP2_S10_R2_001.fastq.gz

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

Alignment Stats

Sequence pairs analysed in total 267531009
Paired-end alignments with a unique best hit 147058074
Pairs without alignments under any condition 79040089
Pairs that did not map uniquely 41432846
Genomic sequence context not extractable (edges of chromosomes) 19080

Cytosine Methylation

Total C's analysed 6007547193
Methylated C's in CpG context 81514938
Methylated C's in CHG context 22267955
Methylated C's in CHH context 104025447
Methylated C's in Unknown context 14712308
Unmethylated C's in CpG context 1013411203
Unmethylated C's in CHG context 1141944448
Unmethylated C's in CHH context 3644383202
Unmethylated C's in Unknown context 73888265
Percentage methylation (CpG context) 7.4%
Percentage methylation (CHG context) 1.9%
Percentage methylation (CHH context) 2.8%
Methylated C's in Unknown context N/A%

Alignment to Individual Bisulfite Strands

OT 38049264 original top strand
CTOT 35288060 complementary to original top strand
CTOB 35314264 complementary to original bottom strand
OB 38387406 original bottom strand

Deduplication

Alignments analysed 147038994
Unique alignments 113077408
Duplicates removed 33961586
Duplicated alignments were found at 23742178 different positions

Cytosine Methylation after Extraction

Total C's analysed 2526322290
Methylated C's in CpG context 33647330
Methylated C's in CHG context 9413140
Methylated C's in CHH context 45509301
Unmethylated C's in CpG context 421628284
Unmethylated C's in CHG context 477529177
Unmethylated C's in CHH context 1538595058
Percentage methylation (CpG context) 7.4%
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 3135828869 171827598 29.32 30.52 18.250
T 3099422238 171532079 28.98 30.46 18.069
C 2077351553 109822870 19.42 19.51 18.915
G 2383308804 109866618 22.28 19.51 21.693
AC 574680515 31579141 5.43 5.61 18.198
CA 660253734 36499708 6.23 6.48 18.089
TC 593226303 32794098 5.60 5.82 18.089
CT 604685036 32992892 5.71 5.86 18.328
CC 413341449 22948860 3.90 4.08 18.011
CG 377925195 17370180 3.57 3.09 21.757
GC 475087863 22490193 4.49 3.99 21.124
GG 529454498 22992004 5.00 4.08 23.028
AG 695465141 33058515 6.57 5.87 21.037
GA 698159490 32859848 6.59 5.84 21.247
TG 752390896 36435058 7.10 6.47 20.650
GT 648688336 31514166 6.12 5.60 20.584
TT 1062480317 63053650 10.03 11.20 16.850
TA 662530956 39235256 6.25 6.97 16.886
AT 751390552 43957702 7.09 7.81 17.093
AA 1092797588 63217613 10.32 11.23 17.286

M-Bias Plot