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Table 4 Hi-Q vs. Standard enzyme variant call comparison

From: Addressing health disparities in Hispanic breast cancer: accurate and inexpensive sequencing of BRCA1 and BRCA2

Sample CHR Location IDS REF VAR Standard QUAL HiQ QUAL Context
Rare coding indels          
DL0099844 chr13 32906535    T Artifact 10.3 No call   T5
DL0099806 chr13 32906547    T Artifact 93.64 No call   T5
DL0099818 chr13 32906547    T No call   Artifact 13  
DL0099791 chr13 32906565    A Artifact 622.5 No call   A6
DL0099802 chr13 32906565    A Artifact 737.8 No call   
DL0099818 chr13 32906565    A Artifact 160.3 No call   
DL0099828 chr13 32906565    A Artifact 793.8 No call   
DL0099833 chr13 32906565    A Artifact 383.3 No call   
DL0099840 chr13 32906565    A Artefact 744.6 No call   
DL0099874 chr13 32906565    A Artefact 458.6 No call   
DL0099818 chr13 32906576    A Artefact 158.9 No call   A5
DL0099879 chr13 32906576    A Artefact 161.1 Artifact 293.2  
DL0099824 chr13 32906576    A No call   Artifact 373.7  
DL0099842 chr13 32906576    A No call   Artifact 212.6  
DL0099846 chr13 32906576    A No call   Artifact 325.6  
DL0099851 chr13 32906576    A No call   Artifact 288.0  
DL0099832 chr13 32906602    A Artifact 101.0 No call   A7
DL0099854 chr13 32906602    A Artifact 80.27 No call   
DL0099812 chr13 32906609    AAT Artifact 11.8 No call   A7T4
DL0099867 chr13 32906609    AT Artifact 19.39 No call   
DL0099873 chr13 32906609    AAT Artifact 20.66 No call   
DL0099879 chr13 32906609    AT Artifact 45.22 No call   
DL0099806 chr13 32906647    A Artifact 32.02 No call   A5
DL0099841 chr13 32906647    A Artifact 33.75 No call   
DL0099808 chr13 32913668    A Artifact 11.78 No call   A4
DL0099791 chr13 32914270   T   Valid 627 Valid 583.7 agTg
DL0099847 chr13 32929161    A Artifact 13.91 No call   A6
DL0099795 chr13 32929287    A Artifact 22.35 No call   A4
DL0099802 chr13 32929287    A Artifact 12.56 No call   
DL0099804 chr13 32929287    A Artifact 14.27 No call   
DL0099816 chr13 32929287    A Artifact 16.41 No call   
DL0099821 chr13 32929287    A Artifact 10.65 No call   
DL0099831 chr13 32929287    A Artifact 10.4 No call   
DL0099839 chr13 32929287    A Artifact 15.97 No call   
DL0099844 chr13 32929287    A Artifact 16.08 No call   
DL0099880 chr13 32929287    A Artifact 20.42 No call   
DL0099874 chr17 41215952 rs80357710 CA   Valid 893 Valid 794.1 CA4
DL0099847 chr17 41256244    T Artifact 13.14 No call   T4
DL0099801 chr17 41276044 rs80359877 CAGATGGGACA   Valid 856 Valid 611.1  
DL0099855 chr17 41276044    CT Valid 483 Valid 608.1  
Rare SNVs           
DL0099801 chr13 32906446 rs28897705 T G Valid 348 Valid 469.2  
DL0099870 chr13 32906571 rs55939572 A C No call   Artifact 41.04  
DL0099797 chr13 32912414 rs80358638 G T Valid 316 Valid 343.4  
DL0099879 chr13 32912553 cosmic:69844,esp,rs80358656 C T Valid 343 Valid 405.2  
DL0099858 chr13 32972695 rs80358387 A G Valid 520.1 Valid 608.6  
DL0099877 chr17 41197756 rs80357323 A C Valid 522.5 Valid 675.3  
DL0099816 chr17 41201181 rs80357069 C T Valid 512 Valid 799.2  
DL0099816 chr17 41201185 rs80357065 A T Valid 519 Valid 805.8  
DL0099879 chr17 41222976 rs80356968 A G Valid 560.3 Valid 495.7  
DL0099858 chr17 41243948 rs56214134 C A Valid 758.5 Valid 698.1  
DL0099836 chr17 41245071 rs28897683 G T Valid 325.6 Valid 248.3  
DL0099801 chr17 41246037 rs56272539 C T Valid 835.4 Valid 998.0  
DL0099838 chr17 41267755   T A Valid 731.1 Valid 910.6  
  1. A set of 91 samples were amplified and the resulting library run on either the standard sequencing enzyme or Hi-Q. Variants were called by TVC4.0 with recommended settings optimized for Hi-Q enzyme (see Methods). Lines in bold were manually validated
  2. REF reference base, VAR variant base. QUAL quality score of variant