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-- A modular tool to aggregate results from bioinformatics analyses across many samples into a single report. -
- - - - - - - - - - - -Report
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- generated on 2023-06-24, 02:09
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- based on data in:
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- /home/sgurr/Airradians_lcWGS/F0_F2_April2023/output/fastp_multiQC/raw
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General Statistics
- - - - - - - - - - - Showing 390/390 rows and 3/5 columns. - -| Sample Name | % Dups | % GC | M Seqs |
|---|---|---|---|
| F0-B10_R1_001 | 38.1% | 36% | 17.6 |
| F0-B10_R2_001 | 36.3% | 37% | 17.6 |
| F0-B11_R1_001 | 35.3% | 37% | 16.1 |
| F0-B11_R2_001 | 34.1% | 37% | 16.1 |
| F0-B13_R1_001 | 36.5% | 37% | 9.7 |
| F0-B13_R2_001 | 35.7% | 37% | 9.7 |
| F0-B14_R1_001 | 36.5% | 36% | 20.4 |
| F0-B14_R2_001 | 35.8% | 36% | 20.4 |
| F0-B15_R1_001 | 34.7% | 37% | 20.4 |
| F0-B15_R2_001 | 34.6% | 37% | 20.4 |
| F0-B16_R1_001 | 34.6% | 36% | 24.2 |
| F0-B16_R2_001 | 33.5% | 36% | 24.2 |
| F0-B17_R1_001 | 31.3% | 37% | 9.2 |
| F0-B17_R2_001 | 30.1% | 37% | 9.2 |
| F0-B18_R1_001 | 42.7% | 37% | 31.6 |
| F0-B18_R2_001 | 42.2% | 37% | 31.6 |
| F0-B19_R1_001 | 33.2% | 37% | 13.5 |
| F0-B19_R2_001 | 31.8% | 37% | 13.5 |
| F0-B1_R1_001 | 37.4% | 37% | 22.7 |
| F0-B1_R2_001 | 37.1% | 37% | 22.7 |
| F0-B20_R1_001 | 36.4% | 36% | 16.0 |
| F0-B20_R2_001 | 35.1% | 37% | 16.0 |
| F0-B21_R1_001 | 35.7% | 37% | 13.3 |
| F0-B21_R2_001 | 34.1% | 37% | 13.3 |
| F0-B23_R1_001 | 31.9% | 37% | 6.9 |
| F0-B23_R2_001 | 30.6% | 37% | 6.9 |
| F0-B24_R1_001 | 30.0% | 36% | 4.7 |
| F0-B24_R2_001 | 28.5% | 37% | 4.7 |
| F0-B25_R1_001 | 39.3% | 37% | 18.4 |
| F0-B25_R2_001 | 38.6% | 37% | 18.4 |
| F0-B27_R1_001 | 36.0% | 37% | 14.6 |
| F0-B27_R2_001 | 35.2% | 37% | 14.6 |
| F0-B2_R1_001 | 41.0% | 38% | 28.2 |
| F0-B2_R2_001 | 40.6% | 37% | 28.2 |
| F0-B3_R1_001 | 40.0% | 37% | 26.0 |
| F0-B3_R2_001 | 38.1% | 37% | 26.0 |
| F0-B4_R1_001 | 39.0% | 37% | 22.5 |
| F0-B4_R2_001 | 37.9% | 37% | 22.5 |
| F0-B5_R1_001 | 38.7% | 37% | 26.1 |
| F0-B5_R2_001 | 37.7% | 37% | 26.1 |
| F0-B6_R1_001 | 33.8% | 36% | 15.6 |
| F0-B6_R2_001 | 31.5% | 37% | 15.6 |
| F0-B7_R1_001 | 38.4% | 37% | 19.0 |
| F0-B7_R2_001 | 38.0% | 37% | 19.0 |
| F0-B9_R1_001 | 36.2% | 36% | 22.6 |
| F0-B9_R2_001 | 35.6% | 37% | 22.6 |
| F1-B1-pH75_R1_001 | 34.9% | 35% | 21.7 |
| F1-B1-pH75_R2_001 | 29.7% | 35% | 21.7 |
| F1-B1-pH8_R1_001 | 32.5% | 35% | 10.6 |
| F1-B1-pH8_R2_001 | 30.6% | 35% | 10.6 |
| F1-B10-pH8_R1_001 | 29.9% | 35% | 12.0 |
| F1-B10-pH8_R2_001 | 27.5% | 36% | 12.0 |
| F1-B11-pH75_R1_001 | 31.0% | 35% | 8.0 |
| F1-B11-pH75_R2_001 | 29.6% | 35% | 8.0 |
| F1-B11-pH8_R1_001 | 32.4% | 35% | 11.4 |
| F1-B11-pH8_R2_001 | 30.9% | 36% | 11.4 |
| F1-B12-pH75_R1_001 | 31.5% | 35% | 9.2 |
| F1-B12-pH75_R2_001 | 30.1% | 36% | 9.2 |
| F1-B12-pH8_R1_001 | 30.8% | 35% | 11.1 |
| F1-B12-pH8_R2_001 | 28.8% | 35% | 11.1 |
| F1-B13-pH75_R1_001 | 38.7% | 35% | 29.8 |
| F1-B13-pH75_R2_001 | 35.0% | 36% | 29.8 |
| F1-B13-pH8_R1_001 | 30.1% | 35% | 9.0 |
| F1-B13-pH8_R2_001 | 27.7% | 36% | 9.0 |
| F1-B14-pH75_R1_001 | 44.9% | 40% | 12.1 |
| F1-B14-pH75_R2_001 | 45.4% | 40% | 12.1 |
| F1-B14-pH8_R1_001 | 31.7% | 35% | 11.1 |
| F1-B14-pH8_R2_001 | 29.8% | 36% | 11.1 |
| F1-B15-pH75_R1_001 | 37.3% | 37% | 17.6 |
| F1-B15-pH75_R2_001 | 36.8% | 37% | 17.6 |
| F1-B15-pH8_R1_001 | 30.3% | 35% | 8.7 |
| F1-B15-pH8_R2_001 | 29.1% | 35% | 8.7 |
| F1-B16-pH75_R1_001 | 35.5% | 35% | 17.9 |
| F1-B16-pH75_R2_001 | 33.5% | 35% | 17.9 |
| F1-B16-pH8_R1_001 | 29.9% | 35% | 10.4 |
| F1-B16-pH8_R2_001 | 29.1% | 36% | 10.4 |
| F1-B17-pH75_R1_001 | 33.1% | 35% | 19.9 |
| F1-B17-pH75_R2_001 | 31.0% | 35% | 19.9 |
| F1-B18-pH75_R1_001 | 51.5% | 35% | 231.3 |
| F1-B18-pH75_R2_001 | 48.9% | 35% | 231.3 |
| F1-B18-pH8_R1_001 | 31.8% | 35% | 12.9 |
| F1-B18-pH8_R2_001 | 30.8% | 36% | 12.9 |
| F1-B2-pH8_R1_001 | 50.0% | 28% | 0.0 |
| F1-B2-pH8_R2_001 | 50.0% | 24% | 0.0 |
| F1-B20-pH75_R1_001 | 34.3% | 35% | 16.0 |
| F1-B20-pH75_R2_001 | 32.8% | 35% | 16.0 |
| F1-B20-pH8_R1_001 | 30.1% | 35% | 9.2 |
| F1-B20-pH8_R2_001 | 28.2% | 36% | 9.2 |
| F1-B21-pH75_R1_001 | 30.0% | 35% | 10.2 |
| F1-B21-pH75_R2_001 | 28.2% | 35% | 10.2 |
| F1-B21-pH8_R1_001 | 29.9% | 35% | 11.0 |
| F1-B21-pH8_R2_001 | 28.6% | 35% | 11.0 |
| F1-B22-pH75_R1_001 | 27.6% | 35% | 0.0 |
| F1-B22-pH75_R2_001 | 25.8% | 36% | 0.0 |
| F1-B23-pH75_R1_001 | 30.9% | 35% | 11.7 |
| F1-B23-pH75_R2_001 | 29.4% | 35% | 11.7 |
| F1-B24-pH8_R1_001 | 32.5% | 35% | 10.8 |
| F1-B24-pH8_R2_001 | 31.5% | 36% | 10.8 |
| F1-B25-pH8_R1_001 | 31.8% | 35% | 8.8 |
| F1-B25-pH8_R2_001 | 30.4% | 35% | 8.8 |
| F1-B3-pH75_R1_001 | 31.8% | 35% | 13.0 |
| F1-B3-pH75_R2_001 | 29.7% | 36% | 13.0 |
| F1-B3-pH8_R1_001 | 30.4% | 35% | 11.3 |
| F1-B3-pH8_R2_001 | 28.2% | 36% | 11.3 |
| F1-B30-pH75_R1_001 | 25.8% | 35% | 0.0 |
| F1-B30-pH75_R2_001 | 24.9% | 35% | 0.0 |
| F1-B4-pH75_R1_001 | 30.3% | 35% | 7.6 |
| F1-B4-pH75_R2_001 | 27.3% | 35% | 7.6 |
| F1-B4-pH8_R1_001 | 29.7% | 35% | 10.5 |
| F1-B4-pH8_R2_001 | 15.5% | 37% | 10.5 |
| F1-B5-pH8_R1_001 | 31.5% | 35% | 18.0 |
| F1-B5-pH8_R2_001 | 29.2% | 36% | 18.0 |
| F1-B6-pH75DUP_R1_001 | 35.3% | 37% | 17.4 |
| F1-B6-pH75DUP_R2_001 | 34.5% | 37% | 17.4 |
| F1-B6-pH75_R1_001 | 41.2% | 41% | 30.7 |
| F1-B6-pH75_R2_001 | 41.4% | 40% | 30.7 |
| F1-B6-pH8_R1_001 | 29.6% | 35% | 6.6 |
| F1-B6-pH8_R2_001 | 28.1% | 35% | 6.6 |
| F1-B7-pH75_R1_001 | 30.7% | 35% | 8.4 |
| F1-B7-pH75_R2_001 | 29.0% | 35% | 8.4 |
| F1-B7-pH8_R1_001 | 32.6% | 35% | 13.3 |
| F1-B7-pH8_R2_001 | 29.9% | 35% | 13.3 |
| F1-B8-pH75_R1_001 | 31.6% | 35% | 8.4 |
| F1-B8-pH75_R2_001 | 30.2% | 35% | 8.4 |
| F1-B8-pH8_R1_001 | 29.7% | 35% | 11.6 |
| F1-B8-pH8_R2_001 | 27.4% | 36% | 11.6 |
| F1-B9-pH75_R1_001 | 31.8% | 35% | 13.1 |
| F1-B9-pH75_R2_001 | 31.4% | 35% | 13.1 |
| F1-B9-pH8_R1_001 | 31.9% | 35% | 12.5 |
| F1-B9-pH8_R2_001 | 30.0% | 35% | 12.5 |
| F1-J105-pH8_R1_001 | 38.7% | 37% | 16.3 |
| F1-J105-pH8_R2_001 | 38.0% | 37% | 16.3 |
| F1-J106-pH8_R1_001 | 37.3% | 37% | 15.9 |
| F1-J106-pH8_R2_001 | 37.6% | 37% | 15.9 |
| F1-J110-pH8_R1_001 | 42.6% | 38% | 23.1 |
| F1-J110-pH8_R2_001 | 43.5% | 37% | 23.1 |
| F1-J111-pH8_R1_001 | 36.3% | 37% | 15.6 |
| F1-J111-pH8_R2_001 | 34.7% | 37% | 15.6 |
| F1-J112-pH8_R1_001 | 38.3% | 37% | 13.9 |
| F1-J112-pH8_R2_001 | 36.9% | 37% | 13.9 |
| F1-J113-pH8_R1_001 | 39.0% | 37% | 21.4 |
| F1-J113-pH8_R2_001 | 38.4% | 37% | 21.4 |
| F1-J114-pH8_R1_001 | 34.3% | 36% | 11.2 |
| F1-J114-pH8_R2_001 | 33.6% | 37% | 11.2 |
| F1-J12-pH8_R1_001 | 39.3% | 37% | 10.8 |
| F1-J12-pH8_R2_001 | 38.6% | 38% | 10.8 |
| F1-J13-pH8_R1_001 | 35.7% | 37% | 10.3 |
| F1-J13-pH8_R2_001 | 34.6% | 37% | 10.3 |
| F1-J14-pH8_R1_001 | 33.9% | 37% | 9.7 |
| F1-J14-pH8_R2_001 | 33.1% | 37% | 9.7 |
| F1-J157-pH8_R1_001 | 36.3% | 37% | 12.3 |
| F1-J157-pH8_R2_001 | 35.2% | 37% | 12.3 |
| F1-J158-pH8_R1_001 | 35.9% | 37% | 18.2 |
| F1-J158-pH8_R2_001 | 35.5% | 36% | 18.2 |
| F1-J16-pH8_R1_001 | 38.6% | 37% | 12.3 |
| F1-J16-pH8_R2_001 | 38.0% | 37% | 12.3 |
| F1-J160-pH8_R1_001 | 41.0% | 37% | 20.4 |
| F1-J160-pH8_R2_001 | 41.0% | 37% | 20.4 |
| F1-J161-pH8_R1_001 | 37.0% | 37% | 14.7 |
| F1-J161-pH8_R2_001 | 35.9% | 37% | 14.7 |
| F1-J162-pH8_R1_001 | 36.8% | 38% | 13.7 |
| F1-J162-pH8_R2_001 | 35.7% | 37% | 13.7 |
| F1-J163-pH8_R1_001 | 41.3% | 38% | 23.6 |
| F1-J163-pH8_R2_001 | 41.0% | 37% | 23.6 |
| F1-J164-pH8_R1_001 | 38.3% | 37% | 14.0 |
| F1-J164-pH8_R2_001 | 37.4% | 37% | 14.0 |
| F1-J17-pH8_R1_001 | 42.1% | 38% | 23.1 |
| F1-J17-pH8_R2_001 | 41.6% | 38% | 23.1 |
| F1-J18-pH8_R1_001 | 39.8% | 37% | 17.7 |
| F1-J18-pH8_R2_001 | 39.2% | 37% | 17.7 |
| F1-J205-pH75_R1_001 | 33.0% | 37% | 8.4 |
| F1-J205-pH75_R2_001 | 32.1% | 37% | 8.4 |
| F1-J206-pH75_R1_001 | 36.5% | 37% | 14.3 |
| F1-J206-pH75_R2_001 | 36.3% | 37% | 14.3 |
| F1-J207-pH75_R1_001 | 38.4% | 38% | 21.4 |
| F1-J207-pH75_R2_001 | 38.3% | 38% | 21.4 |
| F1-J209-pH75_R1_001 | 40.2% | 36% | 21.4 |
| F1-J209-pH75_R2_001 | 40.6% | 37% | 21.4 |
| F1-J210-pH75_R1_001 | 39.6% | 37% | 16.4 |
| F1-J210-pH75_R2_001 | 39.5% | 37% | 16.4 |
| F1-J211-pH75_R1_001 | 29.3% | 37% | 0.5 |
| F1-J211-pH75_R2_001 | 28.0% | 37% | 0.5 |
| F1-J212-pH75_R1_001 | 33.8% | 37% | 10.4 |
| F1-J212-pH75_R2_001 | 33.9% | 37% | 10.4 |
| F1-J256-pH75_R1_001 | 27.9% | 38% | 0.0 |
| F1-J256-pH75_R2_001 | 27.6% | 37% | 0.0 |
| F1-J258-pH75_R1_001 | 43.4% | 38% | 28.5 |
| F1-J258-pH75_R2_001 | 41.4% | 38% | 28.5 |
| F1-J261-pH75_R1_001 | 39.2% | 37% | 17.3 |
| F1-J261-pH75_R2_001 | 38.2% | 37% | 17.3 |
| F1-J262-pH75_R1_001 | 38.1% | 37% | 14.4 |
| F1-J262-pH75_R2_001 | 37.6% | 37% | 14.4 |
| F1-J263-pH75_R1_001 | 38.9% | 38% | 19.2 |
| F1-J263-pH75_R2_001 | 38.4% | 37% | 19.2 |
| F1-J264-pH75_R1_001 | 35.0% | 37% | 15.3 |
| F1-J264-pH75_R2_001 | 34.4% | 37% | 15.3 |
| F1-J306-pH75_R1_001 | 42.5% | 37% | 39.5 |
| F1-J306-pH75_R2_001 | 41.4% | 37% | 39.5 |
| F1-J307-pH75_R1_001 | 39.3% | 37% | 25.9 |
| F1-J307-pH75_R2_001 | 38.6% | 37% | 25.9 |
| F1-J308-pH75_R1_001 | 38.1% | 36% | 20.6 |
| F1-J308-pH75_R2_001 | 36.0% | 36% | 20.6 |
| F1-J311-pH75_R1_001 | 33.6% | 37% | 9.0 |
| F1-J311-pH75_R2_001 | 32.7% | 37% | 9.0 |
| F1-J312-pH75_R1_001 | 37.1% | 37% | 8.5 |
| F1-J312-pH75_R2_001 | 36.4% | 37% | 8.5 |
| F1-J313-pH75_R1_001 | 36.5% | 37% | 12.4 |
| F1-J313-pH75_R2_001 | 35.7% | 37% | 12.4 |
| F1-J314-pH75_R1_001 | 37.1% | 37% | 13.2 |
| F1-J314-pH75_R2_001 | 36.5% | 37% | 13.2 |
| F1-J354-pH75_R1_001 | 34.4% | 39% | 0.0 |
| F1-J354-pH75_R2_001 | 34.4% | 38% | 0.0 |
| F1-J355-pH75_R1_001 | 36.0% | 38% | 5.1 |
| F1-J355-pH75_R2_001 | 36.2% | 38% | 5.1 |
| F1-J361-pH75_R1_001 | 39.5% | 37% | 12.4 |
| F1-J361-pH75_R2_001 | 39.5% | 37% | 12.4 |
| F1-J362-pH75_R1_001 | 43.7% | 38% | 21.6 |
| F1-J362-pH75_R2_001 | 43.5% | 38% | 21.6 |
| F1-J363-pH75_R1_001 | 37.7% | 37% | 11.5 |
| F1-J363-pH75_R2_001 | 37.1% | 37% | 11.5 |
| F1-J364-pH75_R1_001 | 34.1% | 36% | 11.5 |
| F1-J364-pH75_R2_001 | 32.9% | 36% | 11.5 |
| F1-J372-pH75_R1_001 | 38.4% | 37% | 13.1 |
| F1-J372-pH75_R2_001 | 37.7% | 37% | 13.1 |
| F1-J6-pH8_R1_001 | 40.5% | 38% | 18.2 |
| F1-J6-pH8_R2_001 | 40.2% | 37% | 18.2 |
| F1-J65-pH8_R1_001 | 38.9% | 38% | 23.3 |
| F1-J65-pH8_R2_001 | 38.0% | 37% | 23.3 |
| F1-J66-pH8_R1_001 | 39.3% | 38% | 19.5 |
| F1-J66-pH8_R2_001 | 39.0% | 38% | 19.5 |
| F1-J67-pH8_R1_001 | 38.5% | 37% | 17.0 |
| F1-J67-pH8_R2_001 | 37.7% | 37% | 17.0 |
| F1-J68-pH8_R1_001 | 38.7% | 37% | 16.2 |
| F1-J68-pH8_R2_001 | 38.6% | 37% | 16.2 |
| F1-J69-pH8_R1_001 | 36.2% | 36% | 12.5 |
| F1-J69-pH8_R2_001 | 35.5% | 37% | 12.5 |
| F1-J70-pH8_R1_001 | 42.0% | 37% | 15.9 |
| F1-J70-pH8_R2_001 | 41.3% | 37% | 15.9 |
| F1-J71-pH8_R1_001 | 33.3% | 37% | 4.6 |
| F1-J71-pH8_R2_001 | 32.6% | 37% | 4.6 |
| F2-J102-pH8_R1_001 | 23.7% | 36% | 6.3 |
| F2-J102-pH8_R2_001 | 19.2% | 37% | 6.3 |
| F2-J104-pH8_R1_001 | 42.0% | 37% | 9.6 |
| F2-J104-pH8_R2_001 | 36.8% | 38% | 9.6 |
| F2-J105-pH8_R1_001 | 40.2% | 37% | 7.2 |
| F2-J105-pH8_R2_001 | 35.9% | 38% | 7.2 |
| F2-J107-pH8_R1_001 | 37.3% | 36% | 11.4 |
| F2-J107-pH8_R2_001 | 36.1% | 36% | 11.4 |
| F2-J108-pH8_R1_001 | 37.4% | 36% | 9.4 |
| F2-J108-pH8_R2_001 | 37.0% | 36% | 9.4 |
| F2-J109-pH8_R1_001 | 43.7% | 38% | 4.3 |
| F2-J109-pH8_R2_001 | 43.4% | 38% | 4.3 |
| F2-J122-pH8_R1_001 | 36.2% | 36% | 16.5 |
| F2-J122-pH8_R2_001 | 33.9% | 36% | 16.5 |
| F2-J123-pH8_R1_001 | 32.3% | 35% | 19.1 |
| F2-J123-pH8_R2_001 | 29.6% | 36% | 19.1 |
| F2-J125-pH8_R1_001 | 40.1% | 38% | 13.0 |
| F2-J125-pH8_R2_001 | 39.9% | 38% | 13.0 |
| F2-J126-pH8_R1_001 | 32.2% | 35% | 17.7 |
| F2-J126-pH8_R2_001 | 30.6% | 35% | 17.7 |
| F2-J127-pH8_R1_001 | 31.4% | 35% | 16.3 |
| F2-J127-pH8_R2_001 | 29.3% | 35% | 16.3 |
| F2-J141-pH8_R1_001 | 34.2% | 37% | 17.2 |
| F2-J141-pH8_R2_001 | 33.6% | 37% | 17.2 |
| F2-J142-pH8_R1_001 | 36.2% | 36% | 10.5 |
| F2-J142-pH8_R2_001 | 34.2% | 36% | 10.5 |
| F2-J143-pH8_R1_001 | 44.9% | 39% | 13.8 |
| F2-J143-pH8_R2_001 | 43.8% | 39% | 13.8 |
| F2-J144-pH8_R1_001 | 25.1% | 36% | 6.9 |
| F2-J144-pH8_R2_001 | 22.5% | 37% | 6.9 |
| F2-J145-pH8_R1_001 | 35.9% | 35% | 17.5 |
| F2-J145-pH8_R2_001 | 34.8% | 35% | 17.5 |
| F2-J146-pH8_R1_001 | 35.5% | 36% | 12.7 |
| F2-J146-pH8_R2_001 | 34.7% | 36% | 12.7 |
| F2-J147-pH8_R1_001 | 41.2% | 38% | 12.6 |
| F2-J147-pH8_R2_001 | 40.9% | 38% | 12.6 |
| F2-J161-pH7_R1_001 | 54.4% | 40% | 8.7 |
| F2-J161-pH7_R2_001 | 52.7% | 40% | 8.7 |
| F2-J162-pH7_R1_001 | 61.6% | 44% | 31.8 |
| F2-J162-pH7_R2_001 | 62.4% | 42% | 31.8 |
| F2-J163-pH7_R1_001 | 25.7% | 36% | 7.4 |
| F2-J163-pH7_R2_001 | 23.1% | 37% | 7.4 |
| F2-J164-pH7_R1_001 | 39.9% | 39% | 5.5 |
| F2-J164-pH7_R2_001 | 40.5% | 39% | 5.5 |
| F2-J165-pH7_R1_001 | 37.5% | 37% | 15.4 |
| F2-J165-pH7_R2_001 | 36.3% | 37% | 15.4 |
| F2-J166-pH7_R1_001 | 37.0% | 37% | 19.3 |
| F2-J166-pH7_R2_001 | 36.4% | 37% | 19.3 |
| F2-J181-pH7_R1_001 | 64.2% | 42% | 34.7 |
| F2-J181-pH7_R2_001 | 64.8% | 43% | 34.7 |
| F2-J182-pH7_R1_001 | 24.4% | 36% | 5.1 |
| F2-J182-pH7_R2_001 | 22.4% | 36% | 5.1 |
| F2-J184-pH7_R1_001 | 43.2% | 37% | 23.7 |
| F2-J184-pH7_R2_001 | 42.9% | 37% | 23.7 |
| F2-J185-pH7_R1_001 | 41.8% | 41% | 7.0 |
| F2-J185-pH7_R2_001 | 42.2% | 39% | 7.0 |
| F2-J186-pH7_R1_001 | 38.4% | 38% | 8.2 |
| F2-J186-pH7_R2_001 | 37.5% | 38% | 8.2 |
| F2-J187-pH7_R1_001 | 37.4% | 37% | 10.3 |
| F2-J187-pH7_R2_001 | 36.4% | 37% | 10.3 |
| F2-J2-pH75_R1_001 | 26.4% | 35% | 11.5 |
| F2-J2-pH75_R2_001 | 24.1% | 36% | 11.5 |
| F2-J201-pH7_R1_001 | 44.1% | 38% | 15.0 |
| F2-J201-pH7_R2_001 | 43.8% | 38% | 15.0 |
| F2-J202-pH7_R1_001 | 35.7% | 36% | 11.8 |
| F2-J202-pH7_R2_001 | 33.9% | 36% | 11.8 |
| F2-J203-pH7_R1_001 | 48.3% | 43% | 19.1 |
| F2-J203-pH7_R2_001 | 48.9% | 42% | 19.1 |
| F2-J204-pH7_R1_001 | 39.4% | 38% | 8.8 |
| F2-J204-pH7_R2_001 | 39.1% | 38% | 8.8 |
| F2-J205-pH7_R1_001 | 39.6% | 38% | 7.0 |
| F2-J205-pH7_R2_001 | 39.0% | 38% | 7.0 |
| F2-J206-pH7_R1_001 | 39.2% | 37% | 8.7 |
| F2-J206-pH7_R2_001 | 38.9% | 37% | 8.7 |
| F2-J22-pH75_R1_001 | 17.1% | 35% | 1.8 |
| F2-J22-pH75_R2_001 | 13.8% | 36% | 1.8 |
| F2-J221-pH7_R1_001 | 44.0% | 36% | 63.3 |
| F2-J221-pH7_R2_001 | 41.6% | 36% | 63.3 |
| F2-J222-pH7_R1_001 | 44.0% | 36% | 0.0 |
| F2-J222-pH7_R2_001 | 44.0% | 34% | 0.0 |
| F2-J223-pH7_R1_001 | 30.6% | 36% | 9.8 |
| F2-J223-pH7_R2_001 | 28.9% | 36% | 9.8 |
| F2-J224-pH7_R1_001 | 29.8% | 36% | 9.9 |
| F2-J224-pH7_R2_001 | 27.1% | 36% | 9.9 |
| F2-J225-pH7_R1_001 | 40.7% | 39% | 13.9 |
| F2-J225-pH7_R2_001 | 40.6% | 39% | 13.9 |
| F2-J227-pH7_R1_001 | 43.0% | 39% | 10.6 |
| F2-J227-pH7_R2_001 | 42.5% | 39% | 10.6 |
| F2-J228-pH7_R1_001 | 39.1% | 39% | 5.0 |
| F2-J228-pH7_R2_001 | 39.6% | 39% | 5.0 |
| F2-J23-pH75_R1_001 | 31.8% | 36% | 5.1 |
| F2-J23-pH75_R2_001 | 29.4% | 37% | 5.1 |
| F2-J24-pH75_R1_001 | 37.2% | 36% | 16.2 |
| F2-J24-pH75_R2_001 | 35.4% | 36% | 16.2 |
| F2-J25-pH75_R1_001 | 24.5% | 35% | 6.3 |
| F2-J25-pH75_R2_001 | 22.9% | 35% | 6.3 |
| F2-J26-pH75_R1_001 | 39.0% | 36% | 14.5 |
| F2-J26-pH75_R2_001 | 37.2% | 36% | 14.5 |
| F2-J27-pH75_R1_001 | 26.1% | 35% | 5.2 |
| F2-J27-pH75_R2_001 | 23.9% | 36% | 5.2 |
| F2-J3-pH75_R1_001 | 36.2% | 36% | 13.9 |
| F2-J3-pH75_R2_001 | 34.6% | 36% | 13.9 |
| F2-J41-pH75_R1_001 | 43.9% | 37% | 5.0 |
| F2-J41-pH75_R2_001 | 40.1% | 38% | 5.0 |
| F2-J42-pH75_R1_001 | 26.0% | 36% | 6.0 |
| F2-J42-pH75_R2_001 | 23.6% | 37% | 6.0 |
| F2-J43-pH75_R1_001 | 44.0% | 41% | 19.7 |
| F2-J43-pH75_R2_001 | 43.9% | 41% | 19.7 |
| F2-J45-pH75_R1_001 | 37.1% | 38% | 2.3 |
| F2-J45-pH75_R2_001 | 37.2% | 38% | 2.3 |
| F2-J46-pH75_R1_001 | 29.8% | 36% | 11.3 |
| F2-J46-pH75_R2_001 | 28.4% | 36% | 11.3 |
| F2-J47-pH75_R1_001 | 40.8% | 39% | 3.6 |
| F2-J47-pH75_R2_001 | 41.2% | 39% | 3.6 |
| F2-J5-pH75_R1_001 | 38.2% | 36% | 16.5 |
| F2-J5-pH75_R2_001 | 36.5% | 36% | 16.5 |
| F2-J6-pH75_R1_001 | 43.2% | 38% | 5.4 |
| F2-J6-pH75_R2_001 | 43.0% | 38% | 5.4 |
| F2-J61-pH75_R1_001 | 22.7% | 35% | 11.4 |
| F2-J61-pH75_R2_001 | 20.7% | 36% | 11.4 |
| F2-J62-pH75_R1_001 | 39.0% | 37% | 9.0 |
| F2-J62-pH75_R2_001 | 36.9% | 38% | 9.0 |
| F2-J63-pH75_R1_001 | 45.0% | 38% | 7.0 |
| F2-J63-pH75_R2_001 | 44.9% | 38% | 7.0 |
| F2-J64-pH75_R1_001 | 42.9% | 38% | 14.2 |
| F2-J64-pH75_R2_001 | 41.5% | 38% | 14.2 |
| F2-J65-pH75_R1_001 | 29.3% | 35% | 17.7 |
| F2-J65-pH75_R2_001 | 27.6% | 36% | 17.7 |
| F2-J66-pH75_R1_001 | 39.5% | 37% | 6.2 |
| F2-J66-pH75_R2_001 | 39.1% | 37% | 6.2 |
| F2-J67-pH75_R1_001 | 46.2% | 43% | 1.9 |
| F2-J67-pH75_R2_001 | 47.6% | 43% | 1.9 |
| F2-J8-pH75_R1_001 | 32.1% | 38% | 21.0 |
| F2-J8-pH75_R2_001 | 32.0% | 38% | 21.0 |
| F2-J82-pH8_R1_001 | 43.8% | 38% | 6.3 |
| F2-J82-pH8_R2_001 | 39.8% | 39% | 6.3 |
| F2-J83-pH8_R1_001 | 35.0% | 37% | 8.9 |
| F2-J83-pH8_R2_001 | 32.3% | 37% | 8.9 |
| F2-J84-pH8_R1_001 | 36.5% | 36% | 13.4 |
| F2-J84-pH8_R2_001 | 35.4% | 36% | 13.4 |
| F2-J85-pH8_R1_001 | 43.8% | 38% | 6.4 |
| F2-J85-pH8_R2_001 | 42.9% | 38% | 6.4 |
| F2-J86-pH8_R1_001 | 34.0% | 36% | 12.9 |
| F2-J86-pH8_R2_001 | 31.6% | 36% | 12.9 |
| F2-J88-pH8_R1_001 | 46.6% | 42% | 42.2 |
| F2-J88-pH8_R2_001 | 48.0% | 41% | 42.2 |
| F2-J89-pH8_R1_001 | 43.4% | 40% | 32.4 |
| F2-J89-pH8_R2_001 | 44.2% | 39% | 32.4 |
| F2-J9-pH75_R1_001 | 38.6% | 38% | 25.5 |
| F2-J9-pH75_R2_001 | 38.2% | 37% | 25.5 |
FastQC
-FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.
- - - - -- 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).
-
- Sequence Quality Histograms - - - -
- -The mean quality value across each base position in the read.
To enable multiple samples to be plotted on the same graph, only the mean quality -scores are plotted (unlike the box plots seen in FastQC reports).
-Taken from the FastQC help:
-The y-axis on the graph shows the quality scores. The higher the score, the better -the base call. The background of the graph divides the y axis into very good quality -calls (green), calls of reasonable quality (orange), and calls of poor quality (red). -The quality of calls on most platforms will degrade as the run progresses, so it is -common to see base calls falling into the orange area towards the end of a read.
Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).
-
- Per Sequence Quality Scores - - - -
- -The number of reads with average quality scores. Shows if a subset of reads has poor quality.
From the FastQC help:
-The per sequence quality score report allows you to see if a subset of your -sequences have universally low quality values. It is often the case that a -subset of sequences will have universally poor quality, however these should -represent only a small percentage of the total sequences.
Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).
-
- Per Base Sequence Content - - - -
- -The proportion of each base position for which each of the four normal DNA bases has been called.
To enable multiple samples to be shown in a single plot, the base composition data -is shown as a heatmap. The colours represent the balance between the four bases: -an even distribution should give an even muddy brown colour. Hover over the plot -to see the percentage of the four bases under the cursor.
-To see the data as a line plot, as in the original FastQC graph, click on a sample track.
-From the FastQC help:
-Per Base Sequence Content plots out the proportion of each base position in a -file for which each of the four normal DNA bases has been called.
-In a random library you would expect that there would be little to no difference -between the different bases of a sequence run, so the lines in this plot should -run parallel with each other. The relative amount of each base should reflect -the overall amount of these bases in your genome, but in any case they should -not be hugely imbalanced from each other.
-It's worth noting that some types of library will always produce biased sequence -composition, normally at the start of the read. Libraries produced by priming -using random hexamers (including nearly all RNA-Seq libraries) and those which -were fragmented using transposases inherit an intrinsic bias in the positions -at which reads start. This bias does not concern an absolute sequence, but instead -provides enrichement of a number of different K-mers at the 5' end of the reads. -Whilst this is a true technical bias, it isn't something which can be corrected -by trimming and in most cases doesn't seem to adversely affect the downstream -analysis.
Rollover for sample name
- --
- Per Sequence GC Content - - - -
- -The average GC content of reads. Normal random library typically have a - roughly normal distribution of GC content.
From the FastQC help:
-This module measures the GC content across the whole length of each sequence -in a file and compares it to a modelled normal distribution of GC content.
-In a normal random library you would expect to see a roughly normal distribution -of GC content where the central peak corresponds to the overall GC content of -the underlying genome. Since we don't know the the GC content of the genome the -modal GC content is calculated from the observed data and used to build a -reference distribution.
-An unusually shaped distribution could indicate a contaminated library or -some other kinds of biased subset. A normal distribution which is shifted -indicates some systematic bias which is independent of base position. If there -is a systematic bias which creates a shifted normal distribution then this won't -be flagged as an error by the module since it doesn't know what your genome's -GC content should be.
Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).
-
- Per Base N Content - - - -
- -The percentage of base calls at each position for which an N was called.
From the FastQC help:
-If a sequencer is unable to make a base call with sufficient confidence then it will
-normally substitute an N rather than a conventional base call. This graph shows the
-percentage of base calls at each position for which an N was called.
It's not unusual to see a very low proportion of Ns appearing in a sequence, especially -nearer the end of a sequence. However, if this proportion rises above a few percent -it suggests that the analysis pipeline was unable to interpret the data well enough to -make valid base calls.
Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).
-
- Sequence Length Distribution - -
- --
- Sequence Duplication Levels - - - -
- -The relative level of duplication found for every sequence.
From the FastQC Help:
-In a diverse library most sequences will occur only once in the final set. -A low level of duplication may indicate a very high level of coverage of the -target sequence, but a high level of duplication is more likely to indicate -some kind of enrichment bias (eg PCR over amplification). This graph shows -the degree of duplication for every sequence in a library: the relative -number of sequences with different degrees of duplication.
-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.
-In a properly diverse library most sequences should fall into the far left of the -plot in both the red and blue lines. A general level of enrichment, indicating broad -oversequencing in the library will tend to flatten the lines, lowering the low end -and generally raising other categories. More specific enrichments of subsets, or -the presence of low complexity contaminants will tend to produce spikes towards the -right of the plot.
Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).
-
- Overrepresented sequences - - - -
- -The total amount of overrepresented sequences found in each library.
FastQC calculates and lists overrepresented sequences in FastQ files. It would not be -possible to show this for all samples in a MultiQC report, so instead this plot shows -the number of sequences categorized as over represented.
-Sometimes, a single sequence may account for a large number of reads in a dataset. -To show this, the bars are split into two: the first shows the overrepresented reads -that come from the single most common sequence. The second shows the total count -from all remaining overrepresented sequences.
-From the FastQC Help:
-A normal high-throughput library will contain a diverse set of sequences, with no -individual sequence making up a tiny fraction of the whole. Finding that a single -sequence is very overrepresented in the set either means that it is highly biologically -significant, or indicates that the library is contaminated, or not as diverse as you expected.
-FastQC lists all of the sequences which make up more than 0.1% of the total. -To conserve memory only sequences which appear in the first 100,000 sequences are tracked -to the end of the file. It is therefore possible that a sequence which is overrepresented -but doesn't appear at the start of the file for some reason could be missed by this module.
Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).
-
- Adapter Content - - - -
- -The cumulative percentage count of the proportion of your - library which has seen each of the adapter sequences at each position.
Note that only samples with ≥ 0.1% adapter contamination are shown.
-There may be several lines per sample, as one is shown for each adapter -detected in the file.
-From the FastQC Help:
-The plot shows a cumulative percentage count of the proportion -of your library which has seen each of the adapter sequences at each position. -Once a sequence has been seen in a read it is counted as being present -right through to the end of the read so the percentages you see will only -increase as the read length goes on.
Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).
-
- Status Checks - - - -
- -Status for each FastQC section showing whether results seem entirely normal (green), -slightly abnormal (orange) or very unusual (red).
FastQC assigns a status for each section of the report. -These give a quick evaluation of whether the results of the analysis seem -entirely normal (green), slightly abnormal (orange) or very unusual (red).
-It is important to stress that although the analysis results appear to give a pass/fail result, -these evaluations must be taken in the context of what you expect from your library. -A 'normal' sample as far as FastQC is concerned is random and diverse. -Some experiments may be expected to produce libraries which are biased in particular ways. -You should treat the summary evaluations therefore as pointers to where you should concentrate -your attention and understand why your library may not look random and diverse.
-Specific guidance on how to interpret the output of each module can be found in the relevant -report section, or in the FastQC help.
-In this heatmap, we summarise all of these into a single heatmap for a quick overview. -Note that not all FastQC sections have plots in MultiQC reports, but all status checks -are shown in this heatmap.
- 
