Alignment Stats
| Sequence pairs analysed in total |
36956713 |
| Paired-end alignments with a unique best hit |
20684439 |
| Pairs without alignments under any condition |
4733212 |
| Pairs that did not map uniquely |
11539062 |
| Genomic sequence context not extractable (edges of chromosomes) |
2 |
|
|
Cytosine Methylation
| Total C's analysed |
913771245 |
| Methylated C's in CpG context |
21657394 |
| Methylated C's in CHG context |
935651 |
| Methylated C's in CHH context |
4145450 |
| Methylated C's in Unknown context |
109581 |
| Unmethylated C's in CpG context |
89529478 |
| Unmethylated C's in CHG context |
155082000 |
| Unmethylated C's in CHH context |
642421272 |
| Unmethylated C's in Unknown context |
988221 |
| Percentage methylation (CpG context) |
19.5% |
| Percentage methylation (CHG context) |
0.6% |
| Percentage methylation (CHH context) |
0.6% |
| Methylated C's in Unknown context |
10.0% |
|
|
Alignment to Individual Bisulfite Strands
| OT |
10355589 |
original top strand |
| CTOT |
0 |
complementary to original top strand |
| CTOB |
0 |
complementary to original bottom strand |
| OB |
10328848 |
original bottom strand |
|
|
Deduplication
| Alignments analysed |
20684437 |
| Unique alignments |
19287059 |
| Duplicates removed |
1397378 |
| Duplicated alignments were found at 1302581 different positions |
|
|
Cytosine Methylation after Extraction
| Total C's analysed |
682454947 |
| Methylated C's in CpG context |
16122733 |
| Methylated C's in CHG context |
567568 |
| Methylated C's in CHH context |
2550268 |
| Unmethylated C's in CpG context |
67059765 |
| Unmethylated C's in CHG context |
115917390 |
| Unmethylated C's in CHH context |
480237223 |
| Percentage methylation (CpG context) |
19.4% |
| 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 | 1616945953 | 378413849 | 34.52 | 32.06 | 4.273 |
|---|
| T | 1493013717 | 378309330 | 31.87 | 32.05 | 3.947 |
|---|
| C | 746499364 | 211781786 | 15.94 | 17.94 | 3.525 |
|---|
| G | 827897105 | 211810957 | 17.67 | 17.95 | 3.909 |
|---|
| AC | 256060252 | 68264877 | 5.51 | 5.78 | 3.751 |
|---|
| CA | 308417467 | 80836853 | 6.63 | 6.85 | 3.815 |
|---|
| TC | 235224232 | 67705770 | 5.06 | 5.74 | 3.474 |
|---|
| CT | 212647816 | 62481783 | 4.57 | 5.29 | 3.403 |
|---|
| CC | 129277401 | 42358709 | 2.78 | 3.59 | 3.052 |
|---|
| CG | 90464293 | 26104181 | 1.95 | 2.21 | 3.466 |
|---|
| GC | 120557178 | 33452245 | 2.59 | 2.83 | 3.604 |
|---|
| GG | 150439010 | 42378301 | 3.23 | 3.59 | 3.550 |
|---|
| AG | 259197148 | 62424886 | 5.57 | 5.29 | 4.152 |
|---|
| GA | 284001152 | 67679435 | 6.11 | 5.73 | 4.196 |
|---|
| TG | 321876159 | 80903356 | 6.92 | 6.85 | 3.979 |
|---|
| GT | 267011456 | 68300800 | 5.74 | 5.79 | 3.909 |
|---|
| TT | 502360487 | 128294772 | 10.80 | 10.87 | 3.916 |
|---|
| TA | 422771627 | 101400983 | 9.09 | 8.59 | 4.169 |
|---|
| AT | 500554229 | 119230832 | 10.76 | 10.10 | 4.198 |
|---|
| AA | 589958119 | 128492079 | 12.69 | 10.89 | 4.591 |
|---|
|
|
M-Bias Plot
