Bismark

Bismark Processing Report

../output/01.00-E-Peve-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_POR-71-TP2_S9_R1_001.fastq.gz and ../output/01.00-E-Peve-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_POR-71-TP2_S9_R2_001.fastq.gz

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

Alignment Stats

Sequence pairs analysed in total 236709796
Paired-end alignments with a unique best hit 132052904
Pairs without alignments under any condition 66375041
Pairs that did not map uniquely 38281851
Genomic sequence context not extractable (edges of chromosomes) 17665

Cytosine Methylation

Total C's analysed 5285849436
Methylated C's in CpG context 69970819
Methylated C's in CHG context 19181560
Methylated C's in CHH context 91424567
Methylated C's in Unknown context 11983188
Unmethylated C's in CpG context 900501437
Unmethylated C's in CHG context 1011829797
Unmethylated C's in CHH context 3192941256
Unmethylated C's in Unknown context 62425874
Percentage methylation (CpG context) 7.2%
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 34407731 original top strand
CTOT 31419253 complementary to original top strand
CTOB 31482943 complementary to original bottom strand
OB 34725312 original bottom strand

Deduplication

Alignments analysed 132035239
Unique alignments 107462100
Duplicates removed 24573139
Duplicated alignments were found at 17650514 different positions

Cytosine Methylation after Extraction

Total C's analysed 2314697606
Methylated C's in CpG context 30238412
Methylated C's in CHG context 8421891
Methylated C's in CHH context 41618998
Unmethylated C's in CpG context 390301061
Unmethylated C's in CHG context 441271557
Unmethylated C's in CHH context 1402845687
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 3006391565 171827598 29.11 30.52 17.497
T 2990661452 171532079 28.95 30.46 17.435
C 2010290850 109822870 19.46 19.51 18.305
G 2321666666 109866618 22.48 19.51 21.132
AC 554008666 31579141 5.42 5.61 17.544
CA 636555775 36499708 6.22 6.48 17.440
TC 572438510 32794098 5.60 5.82 17.456
CT 583466935 32992892 5.71 5.86 17.685
CC 400486529 22948860 3.92 4.08 17.451
CG 368637679 17370180 3.60 3.09 21.222
GC 462451527 22490193 4.52 3.99 20.562
GG 518046349 22992004 5.07 4.08 22.532
AG 671687526 33058515 6.57 5.87 20.318
GA 675087899 32859848 6.60 5.84 20.544
TG 734721651 36435058 7.18 6.47 20.165
GT 634109420 31514166 6.20 5.60 20.121
TT 1020370714 63053650 9.98 11.20 16.183
TA 634423098 39235256 6.20 6.97 16.170
AT 720378108 43957702 7.04 7.81 16.388
AA 1039416467 63217613 10.16 11.23 16.442

M-Bias Plot