Alignment Stats
| Sequences analysed in total |
6621850 |
| Single-end alignments with a unique best hit |
2930376 |
| Sequences without alignments under any condition |
3395551 |
| Sequences that did not map uniquely |
295923 |
| Genomic sequence context not extractable (edges of chromosomes) |
0 |
|
|
Cytosine Methylation
| Total C's analysed |
52231776 |
| Methylated C's in CpG context |
2140898 |
| Methylated C's in CHG context |
459893 |
| Methylated C's in CHH context |
1758898 |
| Methylated C's in Unknown context |
89454 |
| Unmethylated C's in CpG context |
1375536 |
| Unmethylated C's in CHG context |
13017336 |
| Unmethylated C's in CHH context |
33479215 |
| Unmethylated C's in Unknown context |
239629 |
| Percentage methylation (CpG context) |
60.9% |
| Percentage methylation (CHG context) |
3.4% |
| Percentage methylation (CHH context) |
5.0% |
| Methylated C's in Unknown context |
N/A% |
|
|
Alignment to Individual Bisulfite Strands
| OT |
860106 |
original top strand |
| CTOT |
609299 |
complementary to original top strand |
| CTOB |
604772 |
complementary to original bottom strand |
| OB |
856199 |
original bottom strand |
|
|
Deduplication
| Alignments analysed |
5896187 |
| Unique alignments |
4804013 |
| Duplicates removed |
1092174 |
| Duplicated alignments were found at 829307 different positions |
|
|
Cytosine Methylation after Extraction
| Total C's analysed |
69183265 |
| Methylated C's in CpG context |
2615328 |
| Methylated C's in CHG context |
200866 |
| Methylated C's in CHH context |
544750 |
| Unmethylated C's in CpG context |
1676942 |
| Unmethylated C's in CHG context |
17924236 |
| Unmethylated C's in CHH context |
46221143 |
| Percentage methylation (CpG context) |
60.9% |
| Percentage methylation (CHG context) |
1.1% |
| Percentage methylation (CHH context) |
1.2% |
|
|
Nucleotide Coverage
| Nucleotide Class | Counts Sample | Counts Genome | % in Sample | % in Genome | fold coverage |
|---|
| A | 85258032 | 294005666 | 31.01 | 29.12 | 0.290 |
|---|
| T | 72980804 | 294285704 | 26.54 | 29.15 | 0.248 |
|---|
| C | 54253108 | 210594019 | 19.73 | 20.86 | 0.258 |
|---|
| G | 62489463 | 210590343 | 22.72 | 20.86 | 0.297 |
|---|
| AC | 14436202 | 52532529 | 5.31 | 5.20 | 0.275 |
|---|
| CA | 21268515 | 77472169 | 7.82 | 7.67 | 0.275 |
|---|
| TC | 13922826 | 60093701 | 5.12 | 5.95 | 0.232 |
|---|
| CT | 17492073 | 73354317 | 6.43 | 7.27 | 0.238 |
|---|
| CC | 11418905 | 48375161 | 4.20 | 4.79 | 0.236 |
|---|
| CG | 3395388 | 11392056 | 1.25 | 1.13 | 0.298 |
|---|
| GC | 13852067 | 49592331 | 5.10 | 4.91 | 0.279 |
|---|
| GG | 14466269 | 48349387 | 5.32 | 4.79 | 0.299 |
|---|
| AG | 22588810 | 73308184 | 8.31 | 7.26 | 0.308 |
|---|
| GA | 19199960 | 60059654 | 7.06 | 5.95 | 0.320 |
|---|
| TG | 21307185 | 77540413 | 7.84 | 7.68 | 0.275 |
|---|
| GT | 14274883 | 52588666 | 5.25 | 5.21 | 0.271 |
|---|
| TT | 21256717 | 96125962 | 7.82 | 9.52 | 0.221 |
|---|
| TA | 15607825 | 60525298 | 5.74 | 6.00 | 0.258 |
|---|
| AT | 19142888 | 72216445 | 7.04 | 7.15 | 0.265 |
|---|
| AA | 28231621 | 95948192 | 10.38 | 9.50 | 0.294 |
|---|
|
|
M-Bias Plot
