Sample Summary Information For Experiment (ketchum)
Project Summary
| Project Name | ketchum |
| Machine | HWI-1KL138 |
| Run Folder | 111213_SNL138_0054_Ab01afacxx |
| Flow Cell ID | b01afacxx |
| Platform | |
| Control Software | HiSeq Control Software 1.5.15 |
| Primary Analysis | RTA 1.13.48.0 |
| Secondary Analysis | CASAVA-1.8.2 |
Project Results Summary
| Clusters (Raw) | Clusters(PF) | Yield (MBases) |
|---|---|---|
| 529,876,197 | 529,876,197 | 107,035 |
Barcode-Lane summary
| Barcode-Lane | Sample | Barcode | Lane | Species | Analysis Type | Length | Num Tiles | Genome Directory |
|---|
| ketchum-140_CTTGTA_L2 | ketchum-140 | CTTGTA | 2 | hg19 | 48 | / | ||
| ketchum-140_CTTGTA_L3 | ketchum-140 | CTTGTA | 3 | hg19 | 48 | / | ||
| ketchum-140_CTTGTA_L4 | ketchum-140 | CTTGTA | 4 | hg19 | 48 | / | ||
| ketchum-26_GCCAAT_L2 | ketchum-26 | GCCAAT | 2 | hg19 | 48 | / | ||
| ketchum-26_GCCAAT_L3 | ketchum-26 | GCCAAT | 3 | hg19 | 48 | / | ||
| ketchum-26_GCCAAT_L4 | ketchum-26 | GCCAAT | 4 | hg19 | 48 | / | ||
| ketchum-31_CAGATC_L2 | ketchum-31 | CAGATC | 2 | hg19 | 48 | / | ||
| ketchum-31_CAGATC_L3 | ketchum-31 | CAGATC | 3 | hg19 | 48 | / | ||
| ketchum-31_CAGATC_L4 | ketchum-31 | CAGATC | 4 | hg19 | 48 | / |
Sample Results Summary : Read 1
| Sample Info | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Sample | Sample Yield (Mbases) | Clusters (raw) | Clusters (PF) | 1st Cycle Int (PF) | % intensity after 20 cycles (PF) | % PF Clusters | % Align (PF) | Alignment Score (PF) | % Mismatch Rate (PF) | % >=Q30 bases (PF) | Mean Quality SCore (PF) |
| ketchum-140 | 14,194 | 140,535,592 | 140,535,592 | 1136.33 +/- 5.44 | 86.15 +/- 0.17 | 100.00 | 1.24 | 2.23 | 10.52 | 89.57 | 34.85 |
| ketchum-26 | 24,735 | 244,899,947 | 244,899,947 | 1136.33 +/- 5.44 | 86.15 +/- 0.17 | 100.00 | 2.16 | 3.86 | 10.22 | 92.51 | 36.05 |
| ketchum-31 | 14,589 | 144,440,658 | 144,440,658 | 1136.33 +/- 5.44 | 86.15 +/- 0.17 | 100.00 | 0.07 | 0.19 | 4.65 | 89.54 | 34.48 |
Sample Results Summary : Read 2
| Sample Info | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Sample | Sample Yield (Mbases) | Clusters (raw) | Clusters (PF) | 1st Cycle Int (PF) | % intensity after 20 cycles (PF) | % PF Clusters | % Align (PF) | Alignment Score (PF) | % Mismatch Rate (PF) | % >=Q30 bases (PF) | Mean Quality SCore (PF) |
| ketchum-140 | 14,194 | 140,535,592 | 140,535,592 | 1071 +/- 4.32 | 86.87 +/- 0.25 | 100.00 | 1.21 | 2.00 | 12.02 | 83.66 | 32.95 |
| ketchum-26 | 24,735 | 244,899,947 | 244,899,947 | 1071 +/- 4.32 | 86.87 +/- 0.25 | 100.00 | 2.08 | 3.42 | 11.55 | 88.15 | 34.62 |
| ketchum-31 | 14,589 | 144,440,658 | 144,440,658 | 1071 +/- 4.32 | 86.87 +/- 0.25 | 100.00 | 0.07 | 0.18 | 5.90 | 84.25 | 32.94 |
Expanded Sample Summary : Read 1
| Sample Info | Phasing Info | Raw data | Filtered data | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Sample | Clusters (raw) | % Phasing | % Prephasing | % Mismatch Rate (raw) | % PF Clusters | Cycle 2-4 Av Int (PF) | Cycle 2-10 Av % Loss (PF) | Cycle 10-20 Av % Loss (PF) | % Align (PF) | % Mismatch Rate (PF) | % >=Q30 bases (PF) | Mean Quality SCore (PF) |
| ketchum-140 | 140,535,592 | 0.19 +/- 0.00 | 0.22 +/- 0.00 | 10.52 | 100.00 | 1068.22 +/- 2.30 | 0.97 +/- 0.02 | 0.40 +/- 0.01 | 1.24 | 10.52 | 89.57 | 34.85 |
| ketchum-26 | 244,899,947 | 0.19 +/- 0.00 | 0.22 +/- 0.00 | 10.22 | 100.00 | 1068.22 +/- 2.30 | 0.97 +/- 0.02 | 0.40 +/- 0.01 | 2.16 | 10.22 | 92.51 | 36.05 |
| ketchum-31 | 144,440,658 | 0.19 +/- 0.00 | 0.22 +/- 0.00 | 4.65 | 100.00 | 1068.22 +/- 2.30 | 0.97 +/- 0.02 | 0.40 +/- 0.01 | 0.07 | 4.65 | 89.54 | 34.48 |
Expanded Sample Summary : Read 2
| Sample Info | Phasing Info | Raw data | Filtered data | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Sample | Clusters (raw) | % Phasing | % Prephasing | % Mismatch Rate (raw) | % PF Clusters | Cycle 2-4 Av Int (PF) | Cycle 2-10 Av % Loss (PF) | Cycle 10-20 Av % Loss (PF) | % Align (PF) | % Mismatch Rate (PF) | % >=Q30 bases (PF) | Mean Quality SCore (PF) |
| ketchum-140 | 140,535,592 | 0.20 +/- 0.00 | 0.23 +/- 0.00 | 12.02 | 100.00 | 984.19 +/- 3.21 | 0.97 +/- 0.02 | 0.40 +/- 0.01 | 1.21 | 12.02 | 83.66 | 32.95 |
| ketchum-26 | 244,899,947 | 0.20 +/- 0.00 | 0.23 +/- 0.00 | 11.55 | 100.00 | 984.19 +/- 3.21 | 0.97 +/- 0.02 | 0.40 +/- 0.01 | 2.08 | 11.55 | 88.15 | 34.62 |
| ketchum-31 | 144,440,658 | 0.20 +/- 0.00 | 0.23 +/- 0.00 | 5.90 | 100.00 | 984.19 +/- 3.21 | 0.97 +/- 0.02 | 0.40 +/- 0.01 | 0.07 | 5.90 | 84.25 | 32.94 |
IVC Plots
click hereAll Intensity Plots
click hereMismatch Graphs
click hereMismatch Curves
click hereAdditional Paired Statistics
| Sample Info | Relative Orientation Statistics | Insert Size Statistics (for relative orientation R+) | Insert Statistics (% of individually uniquely alignable pairs) | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Sample | F-: >R2 R1> |
F+: >R1 R2> |
R-: <R2 R1> |
R+: >R1 R2< |
Total | Median | Below-median SD | Above-median SD | Low thresh. | High thresh. | Too small | Too large | Orientation and size OK |
| ketchum-140 | 5,942 (0.39%) |
6,238 (0.41%) |
129,302 (8.41%) |
1,396,820 (90.80%) |
1,538,302 | 178 | 43 | 70 | 101 | 3148 | 0 (0.00%) |
6,758 (0.44%) |
1,390,062 (90.36%) |
| ketchum-26 | 19,298 (0.38%) |
19,793 (0.39%) |
481,518 (9.51%) |
4,540,737 (89.71%) |
5,061,346 | 171 | 40 | 66 | 101 | 653 | 0 (0.00%) |
21,478 (0.42%) |
4,519,259 (89.29%) |
| ketchum-31 | 235 (0.36%) |
252 (0.39%) |
4,742 (7.34%) |
59,358 (91.90%) |
64,587 | 179 | 35 | 59 | 101 | 533 | 11 (0.02%) |
165 (0.26%) |
59,182 (91.63%) |
CASAVA-1.8.2