Bismark

Bismark Processing Report

bis_PICO2_R1.fastq.gz

Data processed at 19:41:01 on 2021-12-21


Alignment Stats

Sequences analysed in total 111088
Single-end alignments with a unique best hit 78636
Sequences without alignments under any condition 24467
Sequences that did not map uniquely 7985
Genomic sequence context not extractable (edges of chromosomes) 0

Cytosine Methylation

Total C's analysed 1555375
Methylated C's in CpG context 50259
Methylated C's in CHG context 9846
Methylated C's in CHH context 26942
Methylated C's in Unknown context 834
Unmethylated C's in CpG context 50887
Unmethylated C's in CHG context 400124
Unmethylated C's in CHH context 1017317
Unmethylated C's in Unknown context 6765
Percentage methylation (CpG context) 49.7%
Percentage methylation (CHG context) 2.4%
Percentage methylation (CHH context) 2.6%
Methylated C's in Unknown context N/A%

Alignment to Individual Bisulfite Strands

OT 16140 original top strand
CTOT 23044 complementary to original top strand
CTOB 23264 complementary to original bottom strand
OB 16188 original bottom strand

Deduplication

Alignments analysed 154836
Unique alignments 154569
Duplicates removed 267
Duplicated alignments were found at 254 different positions

Cytosine Methylation after Extraction

Total C's analysed 2480293
Methylated C's in CpG context 78602
Methylated C's in CHG context 12136
Methylated C's in CHH context 30025
Unmethylated C's in CpG context 75698
Unmethylated C's in CHG context 645508
Unmethylated C's in CHH context 1638324
Percentage methylation (CpG context) 50.9%
Percentage methylation (CHG context) 1.8%
Percentage methylation (CHH context) 1.8%

Nucleotide Coverage

Nucleotide Class Counts Sample Counts Genome% in Sample % in Genome fold coverage
A 2527550 294005666 28.19 29.12 0.009
T 2454008 294285704 27.37 29.15 0.008
C 1901454 210594019 21.20 20.86 0.009
G 2084476 210590343 23.24 20.86 0.010
AC 449996 52532529 5.08 5.20 0.009
CA 688889 77472169 7.77 7.67 0.009
TC 498335 60093701 5.62 5.95 0.008
CT 634691 73354317 7.16 7.27 0.009
CC 437345 48375161 4.93 4.79 0.009
CG 117268 11392056 1.32 1.13 0.010
GC 494135 49592331 5.57 4.91 0.010
GG 496217 48349387 5.60 4.79 0.010
AG 710027 73308184 8.01 7.26 0.010
GA 583552 60059654 6.58 5.95 0.010
TG 736159 77540413 8.30 7.68 0.009
GT 487766 52588666 5.50 5.21 0.009
TT 725479 96125962 8.18 9.52 0.008
TA 464452 60525298 5.24 6.00 0.008
AT 578785 72216445 6.53 7.15 0.008
AA 762177 95948192 8.60 9.50 0.008

M-Bias Plot