Table 2. Analysis of reads across genomic windows.
| Regions with reads in: | ||||||||
|---|---|---|---|---|---|---|---|---|
| Sample | Genome | Assay | Regions | Uniread | SmartMap | % Reg. Inc. | % Inc. Reg. | |
| Simulated 50bp | hg38 | Simulation | 15,498,848 | 10,486,482 | 11,994,872 | 28.74% | 14.38% | |
| Simulated, -k 101 | hg38 | Simulation | 15,498,848 | 10,463,337 | 12,012,046 | 29.07% | 14.80% | |
| Simulated 100bp | hg38 | Simulation | 15,498,848 | 9,956,521 | 11,475,027 | 32.77% | 15.25% | |
| AR7 | Input Rep. 1 | mm10* | MNAse-seq | 13,654,309 | 12,129,867 | 13,243,873 | 33.49% | 9.18% |
| H3K4me3 Rep. 1 | mm10* | ChIP-seq | 13,654,309 | 11,329,858 | 12,999,672 | 27.21% | 14.74% | |
| Input Rep. 2 | mm10* | ChIP-seq | 13,654,309 | 12,115,174 | 13,242,243 | 31.96% | 9.30% | |
| H3K4me3 Rep. 2 | mm10* | ChIP-seq | 13,654,309 | 10,952,182 | 12,750,113 | 27.25% | 16.42% | |
| AR8 | Input | dm3† | MNAse-seq | 698,569 | 617,424 | 681,457 | 17.92% | 10.37% |
| H3K27me3 | dm3† | ChIP-seq | 698,569 | 612,050 | 680,193 | 17.39% | 11.13% | |
| AR9 | Input | mm10† | MNAse-seq | 13,654,309 | 12,214,070 | 13,245,567 | 35.60% | 8.45% |
| H3K4me3 | mm10† | ChIP-seq | 13,654,309 | 11,775,058 | 13,208,421 | 30.83% | 12.17% | |
| H3K9me3 | mm10† | ChIP-seq | 13,654,309 | 12,027,438 | 13,245,567 | 32.11% | 10.04% | |
| H3K27me3 | mm10† | ChIP-seq | 13,654,309 | 12,012,091 | 13,237,339 | 31.99% | 10.20% | |
| AR16 | Input | hg38‡ | MNAse-seq | 15,498,848 | 13,879,635 | 14,629,457 | 34.59% | 5.40% |
| H3K4me1 | hg38‡ | ChIP-seq | 15,498,848 | 13,310,801 | 14,423,602 | 31.07% | 8.36% | |
| H3K4me2 | hg38‡ | ChIP-seq | 15,498,848 | 13,298,178 | 14,443,778 | 30.56% | 8.61% | |
| H3K4me3 | hg38‡ | ChIP-seq | 15,498,848 | 10,338,102 | 12,270,858 | 25.24% | 18.70% | |
| AR17 | Input | hg38‡ | MNAse-seq | 15,498,848 | 13,896,029 | 14,634,051 | 34.56% | 5.31% |
| H3K9me3 | hg38‡ | ChIP-seq | 15,498,848 | 13,856,547 | 14,626,552 | 34.14% | 5.56% | |
| H3K27me3 | hg38‡ | ChIP-seq | 15,498,848 | 13,803,814 | 14,618,351 | 33.66% | 5.90% | |
| ENCODE | Snyder Rep. 1 | hg38 | ATAC-seq | 15,498,848 | 10,389,635 | 11,970,867 | 28.34% | 15.22% |
| Snyder Rep. 2 | hg38 | ATAC-seq | 15,498,848 | 9,772,547 | 11,251,766 | 21.53% | 15.14% | |
| Gingeras Rep. 1 | hg38§ | RNA-seq | 41,929 | 21,755 | 25,711 | 22.85% | 18.18% | |
| Gingeras Rep. 2 | hg38§ | RNA-seq | 41,929 | 12,399 | 14,485 | 11.96% | 16.82% | |
For all except the ENCODE RNA-seq datasets, analysis is conducted on 200bp genomic windows. For ENCODE RNA-seq datasets, analysis is conducted on distinct Refseq genes.
% Reg. Inc.: Percent of the total regions in the SmartMap dataset with increased read depth relative to the Uniread dataset.
% Inc. Reg.: Percent increase in the number of regions with reads in the SmartMap dataset relative to the Uniread dataset.
Genome includes ICeChIP barcodes:
* Series 1.
† Series 2.
‡ Series 3.
§ Genome includes ENCODE ERCC standards.