Table 1 Quality metrics for ten haplotype-resolved assemblies.

From: Structural variant-based pangenome construction has low sensitivity to variability of haplotype-resolved bovine assemblies

Breed or species

Haplotype

Read technology

Size (autosomal size)

Contigs (autosomal contigs)

NG50

PG50

QV

BUSCO (single-copy)

Repeat

Original Braunvieh

Paternal (X)

HiFi

3.15 (2.57)

2108 (107)

56.0

16.2

49.2

95.7 (93.9)

49.39

Paternal (X)

ONT

2.70 (2.48)

2622 (109)

71.6

2.8

40.7

95.2 (93.5)

43.27

Maternal

HiFi

3.11 (2.57)

1706 (105)

47.0

23.6

49.7

95.7 (93.9)

48.95

Maternal

ONT

2.70 (2.48)

2622 (109)

71.6

2.7

40.3

95.1 (93.4)

43.19

Nellore

Paternal (Y)

HiFi

2.95 (2.60)

1217 (52)

94.4

79.1

46.1

93.3 (91.8)

47.81

Paternal (Y)

ONT

2.57 (2.49)

1457 (67)

68.5

64.9

42.4

92.8 (91.3)

42.64

Brown Swiss

Maternal

HiFi

3.07 (2.62)

1045 (58)

86.7

81.1

45.6

95.9 (94.2)

48.43

Maternal

ONT

2.67 (2.48)

1268 (71)

64.0

53.0

42.5

95.3 (93.7)

42.85

gaur

Paternal (X)

HiFi

3.02 (2.52)

1352 (75)

73.5

61.2

48.4

95.7 (94.1)

47.73

Paternal (X)

ONT

2.64 (2.48)

532 (89)

68.1

68.1

41.2

95.1 (93.3)

42.26

Piedmontese

Maternal

HiFi

3.10 (2.56)

1427 (90)

52.0

47.6

48.3

95.8 (94.1)

48.43

Maternal

ONT

2.66 (2.48)

782 (64)

82.8

82.8

40.9

95.3 (93.6)

43.06

Hereford (ARS-UCD1.2)

(N/A)

CLR

2.72 (2.49)

2597 (289)

25.9

N/A

35.8

95.7 (93.9)

42.96

VGP Standards

    

1

0.1

40

90

N/A

  1. The assembly haplotype is either maternal or paternal (indicating either an “X” or “Y” paternal sex chromosome). The ARS-UCD1.2 reference is not haplotype-resolved and lacks sufficient parental data to assess phasing, hence the N/A. Size and contigs refer to the entire genome assembly, while the autosomal values only measure chromosomes 1 through 29. NG50 is the contig N50 using the ARS-UCD1.2 reference sequence as the expected length. PG50 is NG50 after splitting contigs into haplotype-phased blocks. Phasing and QV are determined through merqury using parental and F1 short reads. Scaffolded NG50 is not shown, as all assemblies are effectively end-to-end (excluding centromeres and telomeres), with values greater than 100 Mb. Assemblies are available online107.
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