Table 10 Chimera validation with molecular inversion probes sequencing

Merlot 343 Leaf

Merlot 343 Root

Validation conclusion

Cell layer

Chro-mosome

Position

Expected alleles according to PacBio

Mip validation

Expected alleles according to PacBio

Mip validation

Chimeras on Merlot haplotype ‘Cabernet Franc’

L1

chr04

23 822 006

 C/G

C/G

25/10

C

C

11/0

Validated

L1

chr05

25 416 770

 C/T

C/T

125/24

C

C

45/0

Validated

L1

chr08

22 606 874

T/C

T/C

16/6

T

T

13/0

Validated

L1

chr10

16 298 623

 A/G

A/G

101/10

A

A

25/0

Validated

L1

chr12

8 907 103

 C/A

C/A

34/2

C

C

10/0

Validated

L1

chr12

16 700 578

 A/G

A/G

47/15

A

A/G

11/1

1 unexpected read

L1

chr14

8 620 581

T/C

T/C

190/16

T

T/C

73/1

1 unexpected read

L1

chr14

15 844 322

 C/T

C/T

71/4

C

C

19/0

Validated

L1

chr15

20 162 161

G/A

G/A

11/1

G

G/A

11/1

1 unexpected read

L1

chr18

4 105 052

T/C

T/C

102/6

T

T

15/0

Validated

L2

chr17

7 610 259

 C/T

C/T

6/29

C/T

C/T

4/6

Validated

L2

chr18

12 292 200

G/A

G/A

56/67

G/A

G/A/C

16/27/1

1 unexpected read

Chimeras on Merlot

Haplotype ‘Magdeleine Noire des Charentes’

L1

chr03

3 419 274

T/A

T

75

T

T

16

Invalid

L1

chr05

8 797 586

C/A

C/A

35/5

C

C

18

Validated

L1

chr05

12 819 049

T/A

T/A

61/5

T

T

21

Validated

L1

chr07

16 367 184

C/T

C/T

172/16

C

C

49

Validated

L1

chr08

13 911 900

C/A

C/A/G

67/13/1

C

C

36

1 unexpected read

L1

chr09

7 569 730

A/G

A/G

20/1

A

A

10

Validated by only 1 read

L1

chr10

2 278 377

C/A

C/A

110/18

C

C

47

Validated

L1

chr10

22 333 673

T/A

T/A

53/26

T

T/A

18/6

Confusion on cell layer

L1

chr11

10 357 099

T/C

T/C

26/10

T

T

10

Validated

L1

chr13

22 993 757

T/A

T/A

17/2

T

T/C

10/1

1 unexpected read

L1

chr14

30 136 904

A/G

A/G

25/5

A

A/T

10/1

1 unexpected read

L1

chr17

7 800 769

G/A

G/A

73/4

G

G

21

Validated

L1

chr17

20 480 355

C/T

C/T

123/19

C

C

42

Validated

L2

chr07

20 018 317

G/A

G/A

75/112

G/A

G/A

18/45

Validated

L2

chr08

8 665 113

A/C

A/C

64/132

A/C

A/C

13/23

Validated

L2

chr08

18 095 503

C/T

C/T

51/58

C/T

C/T

17/28

Validated

L2

chr12

14 034 710

T/G

T/G

46/71

T/G

T/G

20/15

Validated

L2

chr14

16 511 432

T/A

T/A

62/179

T/A

T/A

52/51

Validated

L2

chr15

20 391 775

T/G

T/G

38/58

T/G

T/G

8/13

Validated

L2

chr17

17 822 477

C/T

C/T

32/27

C/T

C/T

12/22

Validated