Bismark

Bismark Processing Report

../output/01.00-E-Peve-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_POR-76-TP2_S6_R1_001.fastq.gz and ../output/01.00-E-Peve-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_POR-76-TP2_S6_R2_001.fastq.gz

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

Alignment Stats

Sequence pairs analysed in total 173500998
Paired-end alignments with a unique best hit 98546250
Pairs without alignments under any condition 43820661
Pairs that did not map uniquely 31134087
Genomic sequence context not extractable (edges of chromosomes) 11761

Cytosine Methylation

Total C's analysed 3847749515
Methylated C's in CpG context 47480036
Methylated C's in CHG context 17830772
Methylated C's in CHH context 74535138
Methylated C's in Unknown context 10391621
Unmethylated C's in CpG context 676604903
Unmethylated C's in CHG context 737281551
Unmethylated C's in CHH context 2294017115
Unmethylated C's in Unknown context 38399470
Percentage methylation (CpG context) 6.6%
Percentage methylation (CHG context) 2.4%
Percentage methylation (CHH context) 3.1%
Methylated C's in Unknown context N/A%

Alignment to Individual Bisulfite Strands

OT 28826966 original top strand
CTOT 20227940 complementary to original top strand
CTOB 20261300 complementary to original bottom strand
OB 29218283 original bottom strand

Deduplication

Alignments analysed 98534489
Unique alignments 73450350
Duplicates removed 25084139
Duplicated alignments were found at 16790533 different positions

Cytosine Methylation after Extraction

Total C's analysed 1563269175
Methylated C's in CpG context 18525723
Methylated C's in CHG context 6905820
Methylated C's in CHH context 30157664
Unmethylated C's in CpG context 271414926
Unmethylated C's in CHG context 297821632
Unmethylated C's in CHH context 938443410
Percentage methylation (CpG context) 6.4%
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 2123936149 171827598 29.33 30.52 12.361
T 2082485878 171532079 28.76 30.46 12.141
C 1417833575 109822870 19.58 19.51 12.910
G 1617134153 109866618 22.33 19.51 14.719
AC 395589284 31579141 5.52 5.61 12.527
CA 451928677 36499708 6.30 6.48 12.382
TC 399273997 32794098 5.57 5.82 12.175
CT 406714968 32992892 5.67 5.86 12.327
CC 279696003 22948860 3.90 4.08 12.188
CG 264104796 17370180 3.68 3.09 15.204
GC 327192666 22490193 4.56 3.99 14.548
GG 356088477 22992004 4.97 4.08 15.487
AG 469970628 33058515 6.56 5.87 14.216
GA 471786206 32859848 6.58 5.84 14.358
TG 509675463 36435058 7.11 6.47 13.989
GT 439937168 31514166 6.14 5.60 13.960
TT 704460995 63053650 9.83 11.20 11.172
TA 448888073 39235256 6.26 6.97 11.441
AT 507650688 43957702 7.08 7.81 11.549
AA 735202840 63217613 10.26 11.23 11.630

M-Bias Plot