MHC capture and sequencing metrics
| Sample ID | Sequencer | # SMRT cell per sample | Total sequenced reads | Reads passing quality filters | Reads used in pipeline | MHC-specific reads | % of MHC-specific reads | MHC-specific enrichment (fold) | Normalized MHC-specific reads |
|---|---|---|---|---|---|---|---|---|---|
| PGF + COX | Sequel II | 0.5a | 966,185 | 553,336 | 553,336 | 98,975 | 17.89 | 149.06 | 82,327 |
| EAS-F | Sequel II | 0.5b | 1,051,700 | 595,848 | 595,848 | 271,760 | 45.61 | 380.07 | 97,567 |
| EAS-M | Sequel II | 0.5a | 1,432,295 | 799,875 | 600,000 | 315,453 | 52.58 | 438.13 | 111,471 |
| EAS-P | Sequel II | 1 | 4,834,630 | 1,912,901 | 600,000 | 172,559 | 28.76 | 239.67 | 117,112 |
| AFA | Sequel II | 0.5b | 1,106,650 | 637,925 | 600,000 | 178,484 | 29.75 | 247.89 | 97,500 |
| EUR-F | Sequel | 2 | 1,167,299 | 937,719 | 800,000 | 194,468 | 24.31 | 202.57 | —c |
| EUR-M | Sequel | 3 | 2,008,996 | 1,586,392 | 1,586,392 | 163,881 | 10.33 | 86.09 | —c |
| EUR-P | Sequel | 2 | 1,393,143 | 1,083,856 | 650,000 | 187,084 | 28.78 | 239.85 | —c |
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Samples were sequenced on either the PacBio Sequel or Sequel II. All sequenced reads were processed with the CCS algorithm, retaining only HiFi reads for Sequel II samples, sub-HiFi reads were included for the Sequel samples (reads passing quality filters). The number of reads used in the pipeline (reads used in pipeline) depended on the sequencer and the percentage of MHC-specific reads (% MHC-specific reads) reflects the percent of all reads obtained that aligned to the MHC region. The maximum depth of coverage of the Sequel II samples was targeted to 250× using digital normalization (normalized MHC-specific reads).
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(EAS-F) East-Asian father, (EAS-M) East-Asian mother, (EAS-P) East-Asian proband, (EUR-F) European father, (EUR-M) European mother, (EUR-P) European proband.
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a,bThe higher capacity of the Sequel II allowed for multiple samples to be run together on a single flow cell, as indicated.
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cMHC-specific reads in Sequel samples were not subjected to the digital normalization process due to the high error rate, so all MHC-specific reads were used in subsequent steps.
