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Table 1 Number of detected variants across different variant calling tools

From: Evaluation of whole-genome sequencing of four Chinese crested dogs for variant detection using the ion proton system

  Combined analysis Individual analysisa
  SAMtools UG SAMtools UG HC
  Nr of SNVs (Ti/Tvb) Nr of SNVs (Ti/Tvb) Nr of SNVs (Ti/Tvb) Nr of SNVs (Ti/Tvb) Nr of SNVs (Ti/Tvb)
Total 5 165 528 (2.03) 4 802 404 (1.93) 3 065 136 (2.12) 2 650 589 (2.04) 2 410 162 (2.18)
Filtered 4 255 671 (2.19) 4 471 459 (2.01) 2 280 929 (2.22) 2 525 133 (2.09) 2 363 010 (2.19)
Knowna 1 423 628 (2.39) 1 374 703 (2.40) 860 320 (2.44) 896 616 (2.42) 873 093 (2.44)
Novel 2 832 043 (2.10) 3 096 756 (1.87) 1 420 609 (2.11) 1 628 517 (1.94) 1 489 918 (2.06)
  Nr of INDELs Nr of INDELs Nr of INDELs Nr of INDELs Nr of INDELs
Total 11 750 679 3 539 988 3 778 222 341 366 1 295 497
Filtered 5 635 914 2 764 772 1 157 392 334 763 644 610
Knownc 4 188 4 129 1 493 1 001 1 422
Novel 5 631 726 2 760 643 1 155 899 333 761 643 188
  1. aAverage result from four individuals; bTransition-Transversion ratio; cKnown variants in dog [16], UG UnifiedGenotyper tool, HC HaplotypeCaller tool