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Table 2 Sub-categories of Hemi-SNPs in the IL dataset

From: A hybrid next generation transcript sequencing-based approach to identify allelic and homeolog-specific single nucleotide polymorphisms in allotetraploid white clover

Code

Examples*

Contigs

Singlets

Total

 

Consensus (REF/SC/J5)

Underlying bases

   

H-A1

G/G/R

g | g | g

35756

4110

39866

  

| | a

   

H-A2

G/A/R

g | a | a

1145

245

1390

  

| | g

   

H-A3

K/G/K

g | g | g

930

0

930

  

t | | t

   

H-A4

K/G/R

g | g | g

28

0

28

  

t | | a

   

H-A5

G/T/R

g | t | g

1

10

11

  

| | a

   

H-A6

Y/C/K

c | | g

10

0

10

  

t | | t

   

H-A7

C/T/K

c | | t

73

11

84

  

| | g

   

H-B1

G/R/G

g | g | g

14348

1801

16149

  

| a |

   

H-B2

Y/Y/C

c | c | c

2869

0

2869

  

t | t |

   

H-B3

G/K/T

g | g | t

9320

2149

11469

  

| t |

   

H-B4

R/R/C

a | a | c

5

0

5

  

g | g |

   

H-B5

G/R/T

g | g | t

3

0

3

  

| a |

   

H-B6

M/S/C

c | c | c

19

0

19

  

a | g |

   

H-B7

R/S/C

g | g | c

4

0

4

  

a | c |

   

AH-1

S/S/R

g | g | g

91

0

91

  

c | c | a

   

AH-2

K/W/K

t | | t

4

0

4

  

g | a | g

   

AH-3

C/S/M

c | | c

279

43

322

  

| g | a

   

AH-4

C/M/R

c | a | a

245

50

295

  

| c | g

   

AH-5

C/R/S

c | g | g

17

5

22

  

| a | c

   

Total

  

65147

8424

73571

  1. *The column contains one example from all of the possible similar configurations.
  2. Bold setting indicates non-problematic subcategories as described in the main text.
  3. Code H-Ax indicates no variant nucleotides in SC, variant in J5;
  4. Code H-Bx indicates variant nucleotides in SC, no variant in J5;
  5. Code AH-x indicates asymmetric variation in both SC and J5.
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BMC Genomics

ISSN: 1471-2164

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