Bismark

Bismark Processing Report

bis_PICO9_R1.fastq.gz

Data processed at 20:03:08 on 2021-12-21


Alignment Stats

Sequences analysed in total 747191
Single-end alignments with a unique best hit 516067
Sequences without alignments under any condition 159732
Sequences that did not map uniquely 71392
Genomic sequence context not extractable (edges of chromosomes) 0

Cytosine Methylation

Total C's analysed 9647281
Methylated C's in CpG context 299913
Methylated C's in CHG context 69879
Methylated C's in CHH context 186070
Methylated C's in Unknown context 5238
Unmethylated C's in CpG context 303205
Unmethylated C's in CHG context 2468093
Unmethylated C's in CHH context 6320121
Unmethylated C's in Unknown context 39723
Percentage methylation (CpG context) 49.7%
Percentage methylation (CHG context) 2.8%
Percentage methylation (CHH context) 2.9%
Methylated C's in Unknown context N/A%

Alignment to Individual Bisulfite Strands

OT 121671 original top strand
CTOT 136681 complementary to original top strand
CTOB 136958 complementary to original bottom strand
OB 120757 original bottom strand

Deduplication

Alignments analysed 999642
Unique alignments 994997
Duplicates removed 4645
Duplicated alignments were found at 4295 different positions

Cytosine Methylation after Extraction

Total C's analysed 15275967
Methylated C's in CpG context 470413
Methylated C's in CHG context 83796
Methylated C's in CHH context 199590
Unmethylated C's in CpG context 452987
Unmethylated C's in CHG context 3968574
Unmethylated C's in CHH context 10100607
Percentage methylation (CpG context) 50.9%
Percentage methylation (CHG context) 2.1%
Percentage methylation (CHH context) 1.9%

Nucleotide Coverage

Nucleotide Class Counts Sample Counts Genome% in Sample % in Genome fold coverage
A 16487713 294005666 28.28 29.12 0.056
T 16012458 294285704 27.46 29.15 0.054
C 12298492 210594019 21.09 20.86 0.058
G 13506735 210590343 23.17 20.86 0.064
AC 2915375 52532529 5.06 5.20 0.055
CA 4468567 77472169 7.75 7.67 0.058
TC 3236411 60093701 5.62 5.95 0.054
CT 4125267 73354317 7.16 7.27 0.056
CC 2817398 48375161 4.89 4.79 0.058
CG 737937 11392056 1.28 1.13 0.065
GC 3189415 49592331 5.53 4.91 0.064
GG 3211696 48349387 5.57 4.79 0.066
AG 4611855 73308184 8.00 7.26 0.063
GA 3789055 60059654 6.57 5.95 0.063
TG 4780993 77540413 8.30 7.68 0.062
GT 3163411 52588666 5.49 5.21 0.060
TT 4763723 96125962 8.27 9.52 0.050
TA 3040345 60525298 5.28 6.00 0.050
AT 3781806 72216445 6.56 7.15 0.052
AA 4999759 95948192 8.68 9.50 0.052

M-Bias Plot