AIRRseq Data Overview
This section provides a table with overview of the samples used to generate this report.
The Simpson diversity provides a statistical estimate on the probability of selecting two different sequences when randomly selecting 2 from the dataset.
Clonotypes are derived from a common ancestor. Clonotypes share the same V-J gene combination and exhibit highly similar CDR3 sequences. They are therefore usually able to bind to the same epitopes.
Sample Nr | Sample Name | Sequences | Clonotypes | Simpson Diversity | Avg V identity | Avg J identity |
---|---|---|---|---|---|---|
1 | ERR2567228_L001 | 16759 | 2435 | 0.9998963 | 1 | 1 |
2 | ERR2567229_L001 | 15435 | 2368 | 0.9998876 | 1 | 1 |
3 | ERR2567230_L001 | 15503 | 2582 | 0.9998885 | 1 | 1 |
4 | ERR2567231_L001 | 21872 | 3033 | 0.9999168 | 1 | 1 |
5 | ERR2567232_L001 | 6722 | 1932 | 0.9997606 | 1 | 1 |
6 | ERR2567233_L001 | 22932 | 2782 | 0.9999218 | 1 | 1 |
7 | ERR2567234_L001 | 29662 | 2997 | 0.9999373 | 1 | 1 |
8 | ERR2567235_L001 | 20392 | 2849 | 0.9999120 | 1 | 1 |
9 | ERR2567236_L001 | 20234 | 2826 | 0.9999123 | 1 | 1 |
10 | ERR2567237_L001 | 16042 | 2735 | 0.9998906 | 1 | 1 |
11 | ERR2567238_L001 | 15429 | 2473 | 0.9998887 | 1 | 1 |
12 | ERR2567239_L001 | 14908 | 2597 | 0.9998775 | 1 | 1 |
13 | ERR2567240_L001 | 10429 | 2376 | 0.9998424 | 1 | 1 |
CDRH3 Overlap
This section visualizes overlap between repertoires on CDRH3 amino acid level. Overlap is calculated as number of unique CDR3s common divided by number of total unique CDR3s. Scaling is performed on \(log_{10}\) of the (\(overlap +1\)), at permille scale (i.e. \(x1000\))
Top 10 Clonotypes
This section visualizes the Top 10 clonotypes with the corresponding percentage.
The subsequent Table provides this information in a more readable format.
Sample | 1st | 2nd | 3rd | 4th | 5th | 6th | 7th | 8th | 9th | 10th |
---|---|---|---|---|---|---|---|---|---|---|
ERR2567228_L001 | 191: 0.72% | 634: 0.7% | 172: 0.68% | 115: 0.67% | 133: 0.66% | 243: 0.63% | 80: 0.63% | 132: 0.6% | 613: 0.56% | 207: 0.54% |
ERR2567229_L001 | 214: 0.69% | 258: 0.69% | 405: 0.65% | 155: 0.64% | 173: 0.55% | 82: 0.52% | 102: 0.52% | 261: 0.52% | 65: 0.51% | 521: 0.51% |
ERR2567230_L001 | 256: 0.61% | 396: 0.61% | 98: 0.54% | 273: 0.49% | 138: 0.48% | 54: 0.45% | 168: 0.43% | 231: 0.41% | 63: 0.39% | 66: 0.39% |
ERR2567231_L001 | 251: 0.91% | 489: 0.81% | 184: 0.7% | 267: 0.66% | 137: 0.59% | 102: 0.59% | 283: 0.59% | 146: 0.56% | 192: 0.55% | 213: 0.54% |
ERR2567232_L001 | 1381: 1.83% | 502: 1.56% | 851: 1.49% | 624: 1.44% | 225: 1.06% | 125: 0.89% | 93: 0.76% | 239: 0.68% | 232: 0.49% | 404: 0.49% |
ERR2567233_L001 | 113: 0.74% | 450: 0.72% | 277: 0.68% | 112: 0.61% | 110: 0.61% | 80: 0.56% | 272: 0.55% | 371: 0.55% | 296: 0.54% | 764: 0.51% |
ERR2567234_L001 | 506: 0.89% | 176: 0.75% | 498: 0.66% | 184: 0.65% | 152: 0.59% | 123: 0.56% | 196: 0.55% | 366: 0.55% | 90: 0.53% | 130: 0.47% |
ERR2567235_L001 | 173: 0.8% | 287: 0.64% | 127: 0.62% | 131: 0.6% | 285: 0.6% | 69: 0.55% | 84: 0.51% | 277: 0.48% | 138: 0.45% | 160: 0.45% |
ERR2567236_L001 | 775: 1.49% | 379: 1.08% | 342: 0.99% | 396: 0.88% | 177: 0.86% | 800: 0.61% | 266: 0.58% | 484: 0.57% | 132: 0.52% | 102: 0.51% |
ERR2567237_L001 | 174: 0.79% | 144: 0.62% | 306: 0.57% | 99: 0.55% | 199: 0.52% | 64: 0.49% | 212: 0.49% | 234: 0.47% | 248: 0.46% | 311: 0.43% |
ERR2567238_L001 | 812: 0.76% | 395: 0.71% | 311: 0.68% | 177: 0.54% | 159: 0.51% | 108: 0.47% | 728: 0.45% | 53: 0.45% | 35: 0.43% | 80: 0.42% |
ERR2567239_L001 | 251: 1.09% | 118: 0.93% | 161: 0.87% | 81: 0.8% | 77: 0.79% | 67: 0.76% | 642: 0.74% | 286: 0.73% | 1183: 0.68% | 280: 0.67% |
ERR2567240_L001 | 588: 0.97% | 327: 0.83% | 248: 0.74% | 112: 0.59% | 355: 0.48% | 172: 0.41% | 619: 0.37% | 481: 0.36% | 205: 0.35% | 48: 0.35% |
Clonotype Accumulation Curves
This section visualizes the clonotype composition of each repertoire as a size-sorted accumulation curves.
SHM Rates
Violinplots allow examination of the distribution and composition of a metric. Somatic hypermutation rates provide a firsthand measure on the mutation status and thus affinity maturation levels per sample. In the plot below, the somatic hypermutation of each repertoire is visualized as a violinplot over V gene identity (i.e. % difference to closest germline) with mean indicated by a white point.
Amino Acid Physiochemical Properties
The physiochemical properties provide a swift overview of potential protein interaction metrics. Here we focus on 9 properties of the HCDR3 + somatic hypermutation rates across the V gene.Together these metrics allow a quick interpretation of which changes occur in response of e.g. a vaccination or antigenic stimulus.