Table 1 Quantity and distribution of reads and SNPs for each morphotype

From: Whole-genome resequencing of Cucurbita pepo morphotypes to discover genomic variants associated with morphology and horticulturally valuable traits

Morphotype

No. of clean reads

Coverage

% Mapped

Variable sites

% Mis

Ho

    

No.

% Biallelic

% Monoallelic

  

Pumpkin

107,814,560

37.8

94.1

1,077,816

28.38

71.62

1.79

0.08

Marrow

84,887,546

29.8

93.9

1,136,856

39.13

60.87

6.01

0.12

Cocozelle

96,385,370

33.8

94.0

1,194,461

43.76

56.24

5.44

0.14

Zucchini (yellow)

101,593,207

35.7

94.7

1,045,520

75.02

24.98

2.91

0.21

Zucchini (green)

86,968,548

30.5

95.1

636,918

53.30

46.70

3.83

0.09

Subspecies pepo

95,529,846

33.5

94.4

1,018,314

47.92

52.08

4.00

0.13

Acorn

91,160,816

30.1

94.4

2,421,537

9.17

90.83

4.89

0.06

Scallop

93,992,800

32.9

94.9

2,620,106

27.61

72.39

5.34

0.20

Crookneck

106,734,784

37.4

95.0

2,656,513

22.60

77.40

2.84

0.16

Subspecies ovifera

97,296,133

33.5

94.8

2,566,052

19.79

80.21

4.36

0.14

  1. Number of clean reads after cleaning, genome coverage obtained, percentage of mapped reads, number of variable sites compared to the reference genome (no. of variable sites), percentage of the variable sites that are biallelic (%, that is that have two alleles, one identical, and the other different from that of the reference genome) and monoallelic (%, that is that have only one allele, different to that of the reference genome), and percentage of missing data (Mis), and observed heterozygosity (Ho) for the 3,823,977 variable positions found along the genome for all the morphotypes. Average values for each subspecies are also shown. Notice that reference genome was developed from a C. pepo subps. pepo morphotype green Zucchini Spanish accession18
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