Alignment Stats
| Sequences analysed in total |
431464 |
| Single-end alignments with a unique best hit |
311644 |
| Sequences without alignments under any condition |
90763 |
| Sequences that did not map uniquely |
29057 |
| Genomic sequence context not extractable (edges of chromosomes) |
0 |
|
|
Cytosine Methylation
| Total C's analysed |
6298077 |
| Methylated C's in CpG context |
184439 |
| Methylated C's in CHG context |
53099 |
| Methylated C's in CHH context |
132086 |
| Methylated C's in Unknown context |
2783 |
| Unmethylated C's in CpG context |
184133 |
| Unmethylated C's in CHG context |
1584372 |
| Unmethylated C's in CHH context |
4159948 |
| Unmethylated C's in Unknown context |
23966 |
| Percentage methylation (CpG context) |
50.0% |
| Percentage methylation (CHG context) |
3.2% |
| Percentage methylation (CHH context) |
3.1% |
| Methylated C's in Unknown context |
N/A% |
|
|
Alignment to Individual Bisulfite Strands
| OT |
69773 |
original top strand |
| CTOT |
85621 |
complementary to original top strand |
| CTOB |
85475 |
complementary to original bottom strand |
| OB |
70775 |
original bottom strand |
|
|
Deduplication
| Alignments analysed |
598191 |
| Unique alignments |
594203 |
| Duplicates removed |
3988 |
| Duplicated alignments were found at 3916 different positions |
|
|
Cytosine Methylation after Extraction
| Total C's analysed |
9909823 |
| Methylated C's in CpG context |
286243 |
| Methylated C's in CHG context |
63180 |
| Methylated C's in CHH context |
152154 |
| Unmethylated C's in CpG context |
271913 |
| Unmethylated C's in CHG context |
2523871 |
| Unmethylated C's in CHH context |
6612462 |
| Percentage methylation (CpG context) |
51.3% |
| Percentage methylation (CHG context) |
2.4% |
| Percentage methylation (CHH context) |
2.2% |
|
|
Nucleotide Coverage
| Nucleotide Class | Counts Sample | Counts Genome | % in Sample | % in Genome | fold coverage |
|---|
| A | 10773508 | 294005666 | 28.55 | 29.12 | 0.037 |
|---|
| T | 10472306 | 294285704 | 27.75 | 29.15 | 0.036 |
|---|
| C | 7927458 | 210594019 | 21.01 | 20.86 | 0.038 |
|---|
| G | 8561448 | 210590343 | 22.69 | 20.86 | 0.041 |
|---|
| AC | 1909641 | 52532529 | 5.11 | 5.20 | 0.036 |
|---|
| CA | 2909026 | 77472169 | 7.79 | 7.67 | 0.038 |
|---|
| TC | 2122352 | 60093701 | 5.68 | 5.95 | 0.035 |
|---|
| CT | 2680534 | 73354317 | 7.18 | 7.27 | 0.037 |
|---|
| CC | 1804296 | 48375161 | 4.83 | 4.79 | 0.037 |
|---|
| CG | 444951 | 11392056 | 1.19 | 1.13 | 0.039 |
|---|
| GC | 2008896 | 49592331 | 5.38 | 4.91 | 0.041 |
|---|
| GG | 2009047 | 48349387 | 5.38 | 4.79 | 0.042 |
|---|
| AG | 2959885 | 73308184 | 7.93 | 7.26 | 0.040 |
|---|
| GA | 2422926 | 60059654 | 6.49 | 5.95 | 0.040 |
|---|
| TG | 3053122 | 77540413 | 8.18 | 7.68 | 0.039 |
|---|
| GT | 2033557 | 52588666 | 5.45 | 5.21 | 0.039 |
|---|
| TT | 3152046 | 96125962 | 8.44 | 9.52 | 0.033 |
|---|
| TA | 2029992 | 60525298 | 5.44 | 6.00 | 0.034 |
|---|
| AT | 2499233 | 72216445 | 6.69 | 7.15 | 0.035 |
|---|
| AA | 3298293 | 95948192 | 8.83 | 9.50 | 0.034 |
|---|
|
|
M-Bias Plot
