Table 2 Sample evaluation and sequencing data alignment.

From: Maternal energy insufficiency affects testicular development of the offspring in a swine model

Samples

L0

L28

L120

N0

N28

N120

Raw Reads Number

1.1E + 08

1.1E + 08

1.1E + 08

1.1E + 08

1.1E + 08

1.1E + 08

Raw Bases Number

1.7E + 10

1.6E + 10

1.6E + 10

1.7E + 10

1.7E + 10

1.6E + 10

Clean Reads Number

9.0E + 07

8.4E + 07

8.8E + 07

9.3E + 07

8.6E + 07

8.1E + 07

Clean Bases Number

1.4E + 10

1.3E + 10

1.3E + 10

1.4E + 10

1.3E + 10

1.2E + 10

Clean Reads Rate (%)

80.02

78.72

81.19

82.81

76.3

75.88

Raw Q30 Bases Rate (%)

89.36

87.13

88.4

90.52

86.39

86.11

Clean Q30 Bases Rate (%)

94.86

92.99

93.43

95.27

92.87

92.61

rRNA Reads Number

8.5E + 04

5.0E + 04

1.5E + 05

1.2E + 05

2.6E + 04

3.6E + 04

rRNA Mapping Rate (%)

0.09

0.06

0.17

0.13

0.03

0.04

Total Clean Reads Number

9.0E + 07

8.4E + 07

8.8E + 07

9.3E + 07

8.6E + 07

8.1E + 07

Total Clean Bases Number

1.4E + 10

1.3E + 10

1.3E + 10

1.4E + 10

1.3E + 10

1.2E + 10

Total Q30(%)

94.86

92.99

93.43

95.27

92.87

92.61

Total Reads

9.00E + 07

8.36E + 07

9.13E + 07

9.25E + 07

8.61E + 07

1.19E + 08

Mapped Reads

8.04E + 07

7.42E + 07

8.00E + 07

8.28E + 07

7.65E + 07

1.06E + 08

Mapping Rate

0.8928

0.8873

0.8765

0.8949

0.889

0.8934

Unmapped Reads

9.65E + 06

9.42E + 06

1.13E + 07

9.72E + 06

9.56E + 06

1.26E + 07

MultiMap Reads

6.58E + 06

5.38E + 06

6.09E + 06

6.68E + 06

5.84E + 06

8.44E + 06

MultiMap Rate

0.0731

0.0643

0.0667

0.0722

0.0679

0.0711

  1. L0, L28, and L120 were newborn, 28 d, and 120 d, respectively, in the low energy (LE) group. N0, N28, and N120 were newborn, 28 d, and 120 d, respectively, in the control (CON) group.
  2. Total Reads: the total number of sequences after filtering;
  3. Mapped Reads: the number of sequences in the genome that are aligned;
  4. Mapping Rate: the ratio of the number of sequences in the genome that are aligned;
  5. Unmapped Reads: the number of sequences in the genome that are not aligned;
  6. MultiMap Reads: the number of sequences aligned to multiple locations in the genome;
  7. MultiMap Rate: the ratio of the number of sequences aligned to multiple locations in the genome.
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