Table 2 Read mapping statistics for the raw and trimmed reads generated, which were subsequently aligned to the reference sheep genome (Ovis aries v4.0).

From: Differential gene expression analysis of Dohne Merino sheep naturally infected with Haemonchus contortus

 

Animal ID

No. of raw reads

Trimmed reads

Uniquely mapped reads (%)

Multimapped reads (%)

Overall alignment rate (%)

Resistant

B1. 187 AB

7,965,894

5,559,158

3,214,247 (57.82)

1,666,192 (29.97)

94.52

  

B1. 187 J

7,447,813

5,074,960

2,708,551 (53.37)

1,767,431 (34.83)

94.73

  

B1. 187 I

9,590,003

6,009,903

3,950,891 (65.74)

1,278,329 (21.27)

94.66

  

B1. 187 D

7,854,962

5,093,997

2,725,218 (53.50)

1,725,562 (33.87)

94.59

  

B9. 53A B

7,583,394

5,651,175

3,336,818 (59.05)

1,778,701 (31.47)

96.73

  

B9. 53 J

16,789,624

11,422,203

7,323,414 (64.12)

2,642,892 (23.14)

93.58

  

B9. 53 I

12,587,616

9,542,652

6,166,919 (64.62)

2,385,523 (25.00)

95.23

  

B9. 53 D

8,012,934

5,854,821

3,048,667 (52.07)

2,005,565 (34.25)

92.49

  

B1. 168 AB

17,721,465

11,812,286

6,615,565 (56.01)

3,914,099 (33.13)

95.65

  

B1. 168 J

6,185,352

3,922,609

2,463,263 (62.80)

888,796 (22.66)

92.87

  

B1. 168 I

13,722,078

9,255,769

5,725,563 (61.86)

2,404,803 (25.98)

94.30

  

B1. 168 D

8,473,785

5,903,485

1,523,239 (58.81)

3,471,996 (25.80)

91.90

Average susceptible

     

94.27

  

B1. 98 AB

7,296,397

4,770,376

2,519,079 (52.81)

1,698,361 (35.60)

96.16

  

B1. 98 J

11,252,737

8,303,081

5,168,676 (62.25)

2,159,061 (26.00)

94.39

  

B1. 98 I

10,530,979

6,536,805

4,255,625 (65.10)

1,416,775 (21.67)

94.18

  

B1. 98 D

9,523,918

7,036,388

4,161,585 (59.14)

2,089,198 (29.69)

94.70

  

B1. 219 AB

8,466,211

6,382,151

3,746,061 (58.70)

2,094,638 (32.82)

97.13

  

B1. 219 J

9,220,367

6,322,024

4,163,510 (65.86)

1,382,392 (21.87)

94.55

  

B1. 219 I

8,664,119

6,306,077

4,014,015 (63.65)

1,578,704 (25.03)

94.75

  

B1. 219 D

7,933,451

5,407,087

3,247,718 (60.06)

1,303,874 (24.11)

90.96

  

B9. 181 AB

7,765,002

5,584,427

3,290,056 (58.91)

1,597,743 (28.61)

94.31

  

B9. 181 J

8,647,162

6,253,853

4,143,394 (66.25)

1,309,518 (20.94)

94.33

  

B9. 181 I

10,174,523

6,785,270

4,568,498 (67.33)

1,371,261 (20.21)

95.00

  

B9. 181 D

8,039,140

5,799,281

3,755,201(64.75)

1,542,435(26.60)

97.03

Average

     

94,61

Overall average

     

94.44

  1. The first number represents the animal ID, while the letters indicate the gut segment: AB = abomasum, J = jejunum, I = ileum, D = duodenum.
Back to article page