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Table 1 Summary of alignment of big cat individuals and pools to the domestic cat reference assembly

From: Exploiting genomic synteny in Felidae: cross-species genome alignments and SNV discovery can aid conservation management

Species

Sample ID

Reads mapped (%)

Read depth

Quality filtered SNVs

TsTv ratio

Nucleotide diversity (Ï€)

Cheetah

CHEETAH_NAM1

97.74

5.56

27,854,391

1.82

0.00596

CHEETAH_NAM2

97.44

7.15

31,254,807

1.83

0.00804

CHEETAH_NAM3

97.45

8.55

32,936,565

1.85

0.00940

CHEETAH_TZA1

96.94

7.15

29,981,645

1.81

0.00765

CHEETAH_TZA2

97.41

6.28

27,435,836

1.80

0.00637

CHEETAH_TZA3

97.35

7.33

31,533,437

1.85

0.00801

pool (N = 4)

79.23

43.59

38,246,085

2.12

0.04701

Sumatran tiger

SUM_IDN1

95.20

12.41

2,245,646

1.70

0.00243

SUM_IDN2

96.94

13.43

2,984,324

1.67

0.00237

SUM_IDN3

93.87

11.75

2,213,024

1.79

0.00213

SUM_IDN4

95.43

11.93

2,626,994

1.60

0.00243

SUM_IDN5

94.98

12.51

2,442,662

1.78

0.00194

SUM_USA1

94.47

11.46

2,205,499

1.73

0.00203

SUM_USA2

96.58

12.42

2,361,962

1.68

0.00243

pool (N = 4)

88.84

25.78

18,859,425

2.10

0.00740

Snow leopard

SNOW

91.30

43.59

10,634,946

1.73

0.00246

pool (N = 4)

95.58

50.14

9,340,412

1.83

0.00281