A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
This report has been generated by the nf-core/rnaseq analysis pipeline. For information about how to interpret these results, please see the documentation.
Report
generated on 2024-06-12, 00:01
based on data in:
/projects/tomato_genome/fnb/dataprocessing/SRP487154/nfcore-SL5/work/37/104e7929ccc5f399344c74b3918799
General Statistics
Showing 189/189 rows and 15/19 columns.| Sample Name | M Reads Mapped | dupInt | % Proper Pairs | Error rate | M Non-Primary | M Reads Mapped | % Mapped | % Proper Pairs | M Total seqs | % Aligned | M Aligned | % BP Trimmed | % Dups | % GC | M Seqs |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| SRR27806265 | 48.2 | 0.00% | 88.2% | 0.36% | 4.4 | 43.8 | 100.0% | 100.0% | 43.8 | 76.5% | 21.3 | ||||
| SRR27806265_1 | 5.3% | 64.3% | 45% | 27.8 | |||||||||||
| SRR27806265_2 | 5.3% | 65.5% | 46% | 27.8 | |||||||||||
| SRR27806266 | 44.7 | 0.00% | 89.7% | 0.38% | 3.3 | 41.4 | 100.0% | 100.0% | 41.4 | 89.1% | 20.0 | ||||
| SRR27806266_1 | 4.2% | 69.7% | 42% | 22.5 | |||||||||||
| SRR27806266_2 | 3.5% | 69.6% | 42% | 22.5 | |||||||||||
| SRR27806267 | 50.2 | 0.00% | 88.7% | 0.40% | 4.1 | 46.1 | 100.0% | 100.0% | 46.1 | 85.1% | 22.3 | ||||
| SRR27806267_1 | 4.8% | 75.4% | 43% | 26.2 | |||||||||||
| SRR27806267_2 | 2.4% | 74.2% | 43% | 26.2 | |||||||||||
| SRR27806268 | 46.5 | 0.00% | 91.2% | 0.38% | 2.9 | 43.6 | 100.0% | 100.0% | 43.6 | 91.0% | 21.2 | ||||
| SRR27806268_1 | 4.0% | 74.3% | 42% | 23.3 | |||||||||||
| SRR27806268_2 | 1.8% | 73.6% | 42% | 23.3 | |||||||||||
| SRR27806269 | 42.8 | 0.00% | 91.8% | 0.39% | 2.4 | 40.4 | 100.0% | 100.0% | 40.4 | 86.3% | 19.6 | ||||
| SRR27806269_1 | 4.4% | 81.8% | 43% | 22.8 | |||||||||||
| SRR27806269_2 | 2.7% | 80.0% | 43% | 22.8 | |||||||||||
| SRR27806270 | 41.1 | 0.00% | 90.8% | 0.39% | 2.7 | 38.4 | 100.0% | 100.0% | 38.4 | 86.1% | 18.7 | ||||
| SRR27806270_1 | 4.8% | 74.1% | 43% | 21.7 | |||||||||||
| SRR27806270_2 | 3.0% | 73.0% | 43% | 21.7 | |||||||||||
| SRR27806271 | 48.6 | 0.00% | 90.8% | 0.45% | 3.2 | 45.4 | 100.0% | 100.0% | 45.4 | 84.2% | 22.1 | ||||
| SRR27806271_1 | 4.0% | 68.8% | 44% | 26.2 | |||||||||||
| SRR27806271_2 | 3.7% | 68.4% | 44% | 26.2 | |||||||||||
| SRR27806272 | 46.6 | 0.00% | 89.3% | 0.41% | 3.6 | 42.9 | 100.0% | 100.0% | 42.9 | 88.9% | 20.8 | ||||
| SRR27806272_1 | 3.9% | 73.2% | 42% | 23.4 | |||||||||||
| SRR27806272_2 | 2.9% | 72.5% | 42% | 23.4 | |||||||||||
| SRR27806273 | 131.3 | 0.00% | 35.6% | 0.48% | 73.5 | 57.8 | 100.0% | 99.9% | 57.8 | 79.7% | 23.4 | ||||
| SRR27806273_1 | 1.9% | 54.9% | 44% | 29.4 | |||||||||||
| SRR27806273_2 | 2.6% | 62.0% | 43% | 29.4 | |||||||||||
| SRR27806274 | 49.3 | 0.00% | 90.3% | 0.43% | 3.4 | 45.9 | 100.0% | 100.0% | 45.9 | 86.7% | 22.3 | ||||
| SRR27806274_1 | 5.9% | 74.7% | 43% | 25.7 | |||||||||||
| SRR27806274_2 | 4.3% | 73.5% | 43% | 25.7 | |||||||||||
| SRR27806275 | 47.3 | 0.00% | 90.8% | 0.42% | 3.1 | 44.2 | 100.0% | 100.0% | 44.2 | 84.9% | 21.5 | ||||
| SRR27806275_1 | 6.1% | 71.4% | 43% | 25.3 | |||||||||||
| SRR27806275_2 | 4.4% | 70.7% | 43% | 25.3 | |||||||||||
| SRR27806276 | 54.0 | 0.00% | 90.8% | 0.34% | 3.7 | 50.3 | 100.0% | 100.0% | 50.3 | 86.7% | 24.5 | ||||
| SRR27806276_1 | 5.2% | 74.5% | 44% | 28.3 | |||||||||||
| SRR27806276_2 | 5.1% | 75.8% | 44% | 28.3 | |||||||||||
| SRR27806277 | 48.7 | 0.00% | 90.3% | 0.43% | 3.3 | 45.4 | 100.0% | 100.0% | 45.4 | 89.1% | 22.0 | ||||
| SRR27806277_1 | 3.9% | 67.6% | 43% | 24.7 | |||||||||||
| SRR27806277_2 | 2.7% | 67.2% | 43% | 24.7 | |||||||||||
| SRR27806278 | 48.3 | 0.00% | 88.8% | 0.41% | 4.0 | 44.3 | 100.0% | 100.0% | 44.3 | 86.4% | 21.5 | ||||
| SRR27806278_1 | 4.9% | 70.7% | 43% | 24.8 | |||||||||||
| SRR27806278_2 | 3.4% | 70.3% | 43% | 24.8 | |||||||||||
| SRR27806279 | 50.4 | 0.00% | 89.4% | 0.39% | 3.9 | 46.5 | 100.0% | 100.0% | 46.5 | 89.8% | 22.6 | ||||
| SRR27806279_1 | 3.8% | 73.1% | 42% | 25.1 | |||||||||||
| SRR27806279_2 | 2.7% | 73.3% | 42% | 25.1 | |||||||||||
| SRR27806280 | 55.6 | 0.00% | 90.9% | 0.43% | 3.5 | 52.1 | 100.0% | 100.0% | 52.1 | 91.9% | 25.3 | ||||
| SRR27806280_1 | 3.3% | 72.9% | 42% | 27.5 | |||||||||||
| SRR27806280_2 | 3.0% | 73.4% | 42% | 27.5 | |||||||||||
| SRR27806281 | 56.5 | 0.00% | 82.8% | 0.42% | 7.7 | 48.8 | 100.0% | 100.0% | 48.8 | 89.5% | 23.4 | ||||
| SRR27806281_1 | 3.9% | 75.5% | 42% | 26.2 | |||||||||||
| SRR27806281_2 | 3.4% | 73.8% | 42% | 26.2 | |||||||||||
| SRR27806282 | 45.8 | 0.00% | 88.9% | 0.43% | 3.8 | 42.0 | 100.0% | 100.0% | 42.0 | 79.3% | 20.4 | ||||
| SRR27806282_1 | 2.0% | 59.1% | 44% | 25.7 | |||||||||||
| SRR27806282_2 | 2.1% | 58.1% | 45% | 25.7 | |||||||||||
| SRR27806283 | 48.9 | 0.00% | 89.5% | 0.34% | 3.8 | 45.1 | 100.0% | 100.0% | 45.1 | 87.0% | 21.9 | ||||
| SRR27806283_1 | 4.5% | 73.7% | 43% | 25.2 | |||||||||||
| SRR27806283_2 | 4.0% | 74.0% | 43% | 25.2 | |||||||||||
| SRR27806284 | 55.1 | 0.00% | 85.7% | 0.37% | 5.8 | 49.3 | 100.0% | 100.0% | 49.3 | 92.0% | 23.7 | ||||
| SRR27806284_1 | 2.5% | 67.2% | 42% | 25.7 | |||||||||||
| SRR27806284_2 | 2.4% | 67.0% | 43% | 25.7 | |||||||||||
| SRR27806285 | 46.3 | 0.00% | 77.9% | 0.32% | 8.3 | 38.0 | 100.0% | 100.0% | 38.0 | 82.4% | 18.0 | ||||
| SRR27806285_1 | 4.1% | 72.1% | 44% | 21.9 | |||||||||||
| SRR27806285_2 | 2.7% | 71.3% | 45% | 21.9 | |||||||||||
| SRR27806286 | 64.7 | 0.00% | 70.1% | 0.37% | 15.9 | 48.8 | 100.0% | 100.0% | 48.8 | 86.8% | 22.7 | ||||
| SRR27806286_1 | 2.7% | 68.9% | 43% | 26.1 | |||||||||||
| SRR27806286_2 | 2.5% | 68.6% | 44% | 26.1 | |||||||||||
| SRR27806287 | 55.9 | 0.00% | 88.9% | 0.41% | 4.6 | 51.4 | 100.0% | 100.0% | 51.4 | 90.3% | 24.9 | ||||
| SRR27806287_1 | 2.8% | 73.3% | 42% | 27.6 | |||||||||||
| SRR27806287_2 | 2.7% | 72.3% | 42% | 27.6 | |||||||||||
| SRR27806288 | 36.4 | 0.00% | 90.7% | 0.38% | 2.5 | 34.0 | 100.0% | 100.0% | 34.0 | 67.5% | 16.5 | ||||
| SRR27806288_1 | 5.0% | 67.7% | 47% | 24.5 | |||||||||||
| SRR27806288_2 | 4.1% | 66.7% | 47% | 24.5 | |||||||||||
| SRR27806289 | 52.1 | 0.00% | 91.4% | 0.39% | 3.2 | 48.8 | 100.0% | 100.0% | 48.8 | 92.7% | 23.8 | ||||
| SRR27806289_1 | 2.4% | 68.1% | 42% | 25.7 | |||||||||||
| SRR27806289_2 | 2.3% | 67.8% | 42% | 25.7 | |||||||||||
| SRR27806290 | 51.8 | 0.00% | 90.3% | 0.38% | 3.7 | 48.1 | 100.0% | 100.0% | 48.1 | 89.7% | 23.4 | ||||
| SRR27806290_1 | 3.8% | 72.8% | 42% | 26.1 | |||||||||||
| SRR27806290_2 | 3.5% | 72.0% | 42% | 26.1 | |||||||||||
| SRR27806291 | 52.7 | 0.00% | 86.9% | 0.39% | 5.3 | 47.4 | 100.0% | 100.0% | 47.4 | 88.8% | 22.9 | ||||
| SRR27806291_1 | 3.2% | 70.0% | 42% | 25.8 | |||||||||||
| SRR27806291_2 | 2.9% | 69.1% | 43% | 25.8 | |||||||||||
| SRR27806292 | 52.0 | 0.00% | 87.1% | 0.41% | 5.0 | 47.0 | 100.0% | 100.0% | 47.0 | 86.8% | 22.7 | ||||
| SRR27806292_1 | 2.6% | 68.1% | 43% | 26.1 | |||||||||||
| SRR27806292_2 | 2.2% | 67.1% | 43% | 26.1 | |||||||||||
| SRR27806293 | 23.0 | 0.00% | 90.4% | 0.41% | 1.6 | 21.4 | 100.0% | 100.0% | 21.4 | 40.5% | 10.4 | ||||
| SRR27806293_1 | 7.3% | 44.8% | 54% | 25.8 | |||||||||||
| SRR27806293_2 | 7.2% | 44.8% | 54% | 25.8 | |||||||||||
| SRR27806294 | 51.7 | 0.00% | 91.0% | 0.34% | 3.5 | 48.2 | 100.0% | 100.0% | 48.2 | 93.4% | 23.5 | ||||
| SRR27806294_1 | 3.8% | 75.8% | 42% | 25.2 | |||||||||||
| SRR27806294_2 | 2.7% | 75.7% | 42% | 25.2 | |||||||||||
| SRR27806295 | 42.6 | 0.00% | 88.7% | 0.40% | 3.7 | 38.9 | 100.0% | 100.0% | 38.9 | 66.9% | 18.9 | ||||
| SRR27806295_1 | 4.6% | 60.2% | 48% | 28.2 | |||||||||||
| SRR27806295_2 | 4.5% | 60.6% | 48% | 28.2 | |||||||||||
| SRR27806296 | 51.9 | 0.00% | 89.8% | 0.40% | 3.9 | 48.0 | 100.0% | 100.0% | 48.0 | 89.2% | 23.3 | ||||
| SRR27806296_1 | 4.4% | 67.8% | 42% | 26.1 | |||||||||||
| SRR27806296_2 | 4.3% | 67.7% | 42% | 26.1 | |||||||||||
| SRR27806297 | 52.8 | 0.00% | 90.7% | 0.43% | 3.4 | 49.4 | 100.0% | 100.0% | 49.4 | 86.2% | 24.0 | ||||
| SRR27806297_1 | 5.3% | 70.7% | 43% | 27.8 | |||||||||||
| SRR27806297_2 | 4.8% | 71.2% | 43% | 27.8 | |||||||||||
| SRR27806298 | 56.7 | 0.00% | 91.9% | 0.43% | 3.3 | 53.4 | 100.0% | 100.0% | 53.4 | 91.2% | 26.1 | ||||
| SRR27806298_1 | 3.9% | 73.8% | 42% | 28.6 | |||||||||||
| SRR27806298_2 | 3.6% | 74.3% | 42% | 28.6 | |||||||||||
| SRR27806299 | 53.6 | 0.00% | 89.3% | 0.38% | 4.3 | 49.3 | 100.0% | 100.0% | 49.3 | 91.9% | 24.0 | ||||
| SRR27806299_1 | 3.2% | 70.0% | 42% | 26.1 | |||||||||||
| SRR27806299_2 | 2.8% | 71.1% | 42% | 26.1 | |||||||||||
| SRR27806300 | 55.2 | 0.00% | 91.1% | 0.42% | 3.5 | 51.7 | 100.0% | 100.0% | 51.7 | 89.5% | 25.2 | ||||
| SRR27806300_1 | 5.8% | 73.9% | 42% | 28.1 | |||||||||||
| SRR27806300_2 | 5.1% | 74.2% | 42% | 28.1 | |||||||||||
| SRR27806301 | 36.3 | 0.00% | 91.4% | 0.39% | 2.3 | 34.0 | 100.0% | 100.0% | 34.0 | 63.9% | 16.6 | ||||
| SRR27806301_1 | 4.7% | 56.0% | 48% | 26.0 | |||||||||||
| SRR27806301_2 | 4.5% | 56.4% | 49% | 26.0 | |||||||||||
| SRR27806302 | 55.7 | 0.00% | 88.2% | 0.45% | 4.8 | 50.9 | 100.0% | 100.0% | 50.9 | 83.6% | 24.6 | ||||
| SRR27806302_1 | 5.9% | 74.1% | 43% | 29.4 | |||||||||||
| SRR27806302_2 | 5.3% | 74.2% | 43% | 29.4 | |||||||||||
| SRR27806303 | 48.5 | 0.00% | 90.6% | 0.41% | 3.3 | 45.1 | 100.0% | 100.0% | 45.1 | 87.0% | 22.0 | ||||
| SRR27806303_1 | 2.2% | 65.1% | 43% | 25.2 | |||||||||||
| SRR27806303_2 | 2.1% | 64.6% | 43% | 25.2 | |||||||||||
| SRR27806304 | 43.4 | 0.00% | 88.9% | 0.43% | 3.7 | 39.7 | 100.0% | 100.0% | 39.7 | 75.1% | 19.3 | ||||
| SRR27806304_1 | 5.9% | 67.6% | 45% | 25.7 | |||||||||||
| SRR27806304_2 | 5.3% | 66.0% | 45% | 25.7 | |||||||||||
| SRR27806305 | 58.0 | 0.00% | 87.8% | 0.47% | 5.4 | 52.6 | 100.0% | 99.9% | 52.6 | 85.9% | 25.5 | ||||
| SRR27806305_1 | 3.1% | 71.6% | 43% | 29.7 | |||||||||||
| SRR27806305_2 | 3.4% | 70.1% | 43% | 29.7 | |||||||||||
| SRR27806306 | 30.4 | 0.00% | 87.9% | 0.42% | 2.8 | 27.6 | 100.0% | 100.0% | 27.6 | 53.8% | 13.4 | ||||
| SRR27806306_1 | 4.5% | 49.8% | 50% | 24.8 | |||||||||||
| SRR27806306_2 | 4.5% | 49.4% | 50% | 24.8 | |||||||||||
| SRR27806307 | 45.9 | 0.00% | 89.9% | 0.40% | 3.4 | 42.5 | 100.0% | 100.0% | 42.5 | 81.0% | 20.6 | ||||
| SRR27806307_1 | 3.0% | 65.0% | 44% | 25.5 | |||||||||||
| SRR27806307_2 | 2.9% | 64.0% | 44% | 25.5 | |||||||||||
| SRR27806308 | 53.9 | 0.00% | 88.4% | 0.42% | 4.7 | 49.1 | 100.0% | 100.0% | 49.1 | 90.0% | 23.8 | ||||
| SRR27806308_1 | 2.7% | 69.0% | 42% | 26.5 | |||||||||||
| SRR27806308_2 | 2.7% | 67.9% | 42% | 26.5 | |||||||||||
| SRR27806309 | 49.6 | 0.00% | 89.1% | 0.39% | 4.1 | 45.5 | 100.0% | 100.0% | 45.5 | 90.5% | 22.1 | ||||
| SRR27806309_1 | 2.7% | 67.5% | 42% | 24.5 | |||||||||||
| SRR27806309_2 | 2.7% | 66.4% | 42% | 24.5 | |||||||||||
| SRR27806310 | 29.9 | 0.00% | 89.1% | 0.40% | 2.4 | 27.5 | 100.0% | 100.0% | 27.5 | 53.4% | 13.3 | ||||
| SRR27806310_1 | 5.0% | 47.9% | 50% | 25.0 | |||||||||||
| SRR27806310_2 | 5.0% | 48.0% | 50% | 25.0 | |||||||||||
| SRR27806311 | 53.6 | 0.00% | 87.4% | 0.41% | 5.1 | 48.5 | 100.0% | 100.0% | 48.5 | 89.3% | 23.5 | ||||
| SRR27806311_1 | 3.2% | 68.9% | 42% | 26.3 | |||||||||||
| SRR27806311_2 | 3.3% | 68.9% | 42% | 26.3 | |||||||||||
| SRR27806312 | 19.6 | 0.00% | 91.3% | 0.40% | 1.2 | 18.4 | 100.0% | 100.0% | 18.4 | 36.6% | 9.0 | ||||
| SRR27806312_1 | 6.0% | 44.2% | 54% | 24.5 | |||||||||||
| SRR27806312_2 | 5.8% | 44.3% | 54% | 24.5 | |||||||||||
| SRR27806313 | 54.3 | 0.00% | 87.5% | 0.37% | 5.3 | 49.0 | 100.0% | 100.0% | 49.0 | 91.9% | 23.8 | ||||
| SRR27806313_1 | 2.7% | 69.0% | 42% | 25.9 | |||||||||||
| SRR27806313_2 | 2.5% | 69.8% | 42% | 25.9 | |||||||||||
| SRR27806314 | 53.1 | 0.00% | 87.8% | 0.35% | 5.0 | 48.2 | 100.0% | 100.0% | 48.2 | 92.2% | 23.3 | ||||
| SRR27806314_1 | 3.0% | 69.5% | 42% | 25.3 | |||||||||||
| SRR27806314_2 | 2.5% | 70.3% | 42% | 25.3 | |||||||||||
| SRR27806315 | 50.9 | 0.00% | 89.3% | 0.35% | 4.1 | 46.8 | 100.0% | 100.0% | 46.8 | 90.2% | 22.8 | ||||
| SRR27806315_1 | 4.1% | 71.5% | 42% | 25.2 | |||||||||||
| SRR27806315_2 | 3.3% | 71.8% | 42% | 25.2 | |||||||||||
| SRR27806316 | 48.6 | 0.00% | 88.8% | 0.31% | 4.2 | 44.4 | 100.0% | 100.0% | 44.4 | 91.7% | 21.6 | ||||
| SRR27806316_1 | 2.6% | 74.0% | 42% | 23.5 | |||||||||||
| SRR27806316_2 | 1.7% | 74.2% | 42% | 23.5 | |||||||||||
| SRR27806317 | 53.4 | 0.00% | 91.2% | 0.37% | 3.4 | 49.9 | 100.0% | 100.0% | 49.9 | 92.6% | 24.4 | ||||
| SRR27806317_1 | 2.4% | 73.1% | 42% | 26.3 | |||||||||||
| SRR27806317_2 | 2.3% | 73.3% | 42% | 26.3 | |||||||||||
| SRR27806318 | 51.3 | 0.00% | 88.4% | 0.42% | 4.5 | 46.9 | 100.0% | 100.0% | 46.9 | 86.7% | 22.7 | ||||
| SRR27806318_1 | 4.9% | 68.2% | 43% | 26.2 | |||||||||||
| SRR27806318_2 | 4.6% | 67.7% | 43% | 26.2 | |||||||||||
| SRR27806319 | 54.1 | 0.00% | 85.8% | 0.41% | 6.0 | 48.1 | 100.0% | 100.0% | 48.1 | 88.9% | 23.2 | ||||
| SRR27806319_1 | 3.1% | 74.6% | 42% | 26.1 | |||||||||||
| SRR27806319_2 | 2.7% | 73.1% | 42% | 26.1 | |||||||||||
| SRR27806320 | 49.8 | 0.00% | 89.0% | 0.41% | 4.0 | 45.8 | 100.0% | 100.0% | 45.8 | 87.7% | 22.2 | ||||
| SRR27806320_1 | 3.1% | 73.6% | 42% | 25.3 | |||||||||||
| SRR27806320_2 | 2.6% | 72.5% | 42% | 25.3 | |||||||||||
| SRR27806321 | 45.9 | 0.00% | 90.1% | 0.41% | 3.3 | 42.6 | 100.0% | 100.0% | 42.6 | 79.4% | 20.7 | ||||
| SRR27806321_1 | 2.9% | 62.3% | 45% | 26.0 | |||||||||||
| SRR27806321_2 | 3.0% | 62.0% | 45% | 26.0 | |||||||||||
| SRR27806322 | 29.1 | 0.00% | 81.2% | 0.42% | 4.4 | 24.7 | 100.0% | 100.0% | 24.7 | 45.9% | 11.8 | ||||
| SRR27806322_1 | 6.0% | 53.5% | 52% | 25.7 | |||||||||||
| SRR27806322_2 | 5.8% | 53.0% | 52% | 25.7 | |||||||||||
| SRR27806323 | 46.3 | 0.00% | 83.7% | 0.39% | 6.1 | 40.2 | 100.0% | 100.0% | 40.2 | 75.5% | 19.4 | ||||
| SRR27806323_1 | 3.7% | 65.0% | 42% | 25.7 | |||||||||||
| SRR27806323_2 | 3.4% | 64.6% | 43% | 25.7 | |||||||||||
| SRR27806324 | 12.5 | 0.00% | 90.2% | 0.38% | 0.9 | 11.6 | 100.0% | 100.0% | 11.6 | 24.8% | 5.6 | ||||
| SRR27806324_1 | 7.5% | 33.8% | 57% | 22.6 | |||||||||||
| SRR27806324_2 | 7.4% | 33.9% | 57% | 22.6 | |||||||||||
| SRR27806325 | 49.7 | 0.00% | 89.4% | 0.40% | 3.8 | 46.0 | 100.0% | 100.0% | 46.0 | 87.6% | 22.2 | ||||
| SRR27806325_1 | 3.4% | 71.0% | 42% | 25.4 | |||||||||||
| SRR27806325_2 | 3.0% | 70.5% | 42% | 25.4 | |||||||||||
| SRR27806326 | 33.6 | 0.00% | 90.0% | 0.38% | 2.5 | 31.1 | 100.0% | 100.0% | 31.1 | 68.4% | 15.1 | ||||
| SRR27806326_1 | 5.1% | 58.6% | 46% | 22.1 | |||||||||||
| SRR27806326_2 | 4.5% | 57.5% | 46% | 22.1 | |||||||||||
| SRR27806327 | 48.5 | 0.00% | 89.8% | 0.39% | 3.6 | 44.9 | 100.0% | 100.0% | 44.9 | 90.5% | 21.8 | ||||
| SRR27806327_1 | 2.0% | 68.6% | 42% | 24.1 | |||||||||||
| SRR27806327_2 | 1.9% | 67.9% | 42% | 24.1 |
STAR_SALMON DESeq2 PCA plot
PCA plot between samples in the experiment. These values are calculated using DESeq2 in the deseq2_qc.r script.
STAR_SALMON DESeq2 sample similarity
is generated from clustering by Euclidean distances between DESeq2 rlog values for each sample in the deseq2_qc.r script.
DupRadar
provides duplication rate quality control for RNA-Seq datasets. Highly expressed genes can be expected to have a lot of duplicate reads, but high numbers of duplicates at low read counts can indicate low library complexity with technical duplication. This plot shows the general linear models - a summary of the gene duplication distributions.
Preseq
Preseq estimates the complexity of a library, showing how many additional unique reads are sequenced for increasing total read count. A shallow curve indicates complexity saturation. The dashed line shows a perfectly complex library where total reads = unique reads.
Complexity curve
Note that the x axis is trimmed at the point where all the datasets show 80% of their maximum y-value, to avoid ridiculous scales.
RSeQC
RSeQC package provides a number of useful modules that can comprehensively evaluate high throughput RNA-seq data.
Read Distribution
Read Distribution calculates how mapped reads are distributed over genome features.
Inner Distance
Inner Distance calculates the inner distance (or insert size) between two paired RNA reads. Note that this can be negative if fragments overlap.
Read Duplication
read_duplication.py calculates how many alignment positions have a certain number of exact duplicates. Note - plot truncated at 500 occurrences and binned.
Junction Annotation
Junction annotation compares detected splice junctions to a reference gene model. An RNA read can be spliced 2 or more times, each time is called a splicing event.
Junction Saturation
Junction Saturation counts the number of known splicing junctions that are observed in each dataset. If sequencing depth is sufficient, all (annotated) splice junctions should be rediscovered, resulting in a curve that reaches a plateau. Missing low abundance splice junctions can affect downstream analysis.
Infer experiment
Infer experiment counts the percentage of reads and read pairs that match the strandedness of overlapping transcripts. It can be used to infer whether RNA-seq library preps are stranded (sense or antisense).
Bam Stat
All numbers reported in millions.
Samtools
Samtools is a suite of programs for interacting with high-throughput sequencing data.
Percent Mapped
Alignment metrics from samtools stats; mapped vs. unmapped reads.
For a set of samples that have come from the same multiplexed library, similar numbers of reads for each sample are expected. Large differences in numbers might indicate issues during the library preparation process. Whilst large differences in read numbers may be controlled for in downstream processings (e.g. read count normalisation), you may wish to consider whether the read depths achieved have fallen below recommended levels depending on the applications.
Low alignment rates could indicate contamination of samples (e.g. adapter sequences), low sequencing quality or other artefacts. These can be further investigated in the sequence level QC (e.g. from FastQC).
Alignment metrics
This module parses the output from samtools stats. All numbers in millions.
Samtools Flagstat
This module parses the output from samtools flagstat. All numbers in millions.
Mapped reads per contig
The samtools idxstats tool counts the number of mapped reads per chromosome / contig. Chromosomes with < 0.1% of the total aligned reads are omitted from this plot.
Cutadapt
Cutadapt is a tool to find and remove adapter sequences, primers, poly-Atails and other types of unwanted sequence from your high-throughput sequencing reads.
Filtered Reads
This plot shows the number of reads (SE) / pairs (PE) removed by Cutadapt.
Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).
Trimmed Sequence Lengths
This plot shows the number of reads with certain lengths of adapter trimmed.
Obs/Exp shows the raw counts divided by the number expected due to sequencing errors. A defined peak may be related to adapter length.
See the cutadapt documentation for more information on how these numbers are generated.
Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).
FastQC (trimmed)
FastQC (trimmed) This section of the report shows FastQC results after adapter trimming.
Sequence Counts
Sequence counts for each sample. Duplicate read counts are an estimate only.
This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).
You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:
Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.
The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.
Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).