Table 1 Markers used in this study

45 × 8

PDR1

Many missing scores, Cy3/Cy5 false positive problem

No

45 × 15

PDR1

Good

Yes

45 × 20

PDR1

Very weak signals, Cy3/Cy5 false positive problem

No

45 × 29

PDR1

Very weak signals, Cy3/Cy5 false positive problem

No

45 × 31

PDR1

Slight false positive problem

Yes

45 × 33

PDR1

Slight Cy5 false positive problem

Yes

45 × 38

PDR1

Very low polymorphism, Cy5 false positive problem

No

64 × 11

PDR1

Many weak or mixed Cy3/Cy5 scores

No

64 × 14

PDR1

Rather low polymorphism

Yes

64 × 15

PDR1

Many weak or mixed Cy3/Cy5 scores, Cy5 false positive problem

No

64 × 29

PDR1

Very low polymorphism, Cy3 false positive problem

No

64 × 40

PDR1

Many weak or mixed Cy3/Cy5 scores, false positive problem

No

64 × 45

PDR1

Many mixed Cy3/Cy5 scores, Cy5 false positive problem

No

64 × 74

PDR1

Many mixed Cy3/Cy5 scores, false positive problem

No

64 × 76

PDR1

Rather low polymorphism

Yes

95 × 2

PDR1

Slight Cy5 false positive problem

Yes

95 × 19

PDR1

Good

Yes

95 × 25

PDR1

Slight Cy5 false positive problem

Yes

95 × 43

PDR1

Good

Yes

261 × 1

PDR1

No polymorphism

No

261 × 13

PDR1

Cy5 false positive problem, very low polymorphism

No

281 × 1

PDR1

Slight Cy3 false positive problem

Yes

281 × 5

PDR1

Rather low polymorphism

Yes

281 × 16

PDR1

Good

Yes

281 × 40

PDR1

Slight Cy5 false positive problem

Yes

281 × 44

PDR1

Good

Yes

399-3-6

PDR1

Cy3 false positive problem, very low polymorphism

No

399-14-9

PDR1

Good

Yes

399-80-46

PDR1

Slight Cy5 false positive problem

Yes

399-9x

PDR1

Slight Cy5 false positive problem

Yes

399 × 131

PDR1

Slight false positive problem

Yes

399 × 149

PDR1

Slight false positive problem

Yes

1006nr2

PDR1

Low polymorphism; Cy3 false positive problem

No

1006nr9

PDR1

Very poor image

No

1006nr13

PDR1

Good

Yes

1006nr27

PDR1

Good

Yes

1006nr32

PDR1

Weak signal; multiple spot colours

No

1006 × 6

PDR1

Slight Cy5 false positive problem

Yes

1006 × 19

PDR1

Low polymorphism; Cy5 false positives problem

No

1006 × 21

PDR1

Slight Cy3 false positive problem

Yes

1006 × 36

PDR1

Many signals weak or absent; Cy5 false positive problem

No

1006 × 50

PDR1

Some Cy5 background signal (Yellow spots)

Yes

1006 × 58

PDR1

Some Cy5 background signal (Yellow spots)

Yes

1794-1

PDR1

Good

Yes

1794-2

PDR1

Good

Yes

1794 × 7

PDR1

Slight Cy3 false positive problem

Yes

1794 × 9

PDR1

Very low polymorphism

No

1794 × 35

PDR1

Many signals absent; Cy5 background signal

No

2055nr1

PDR1

Good

Yes

2055nr16

PDR1

Low polymorphism, good otherwise

Yes

2055nr23

PDR1

Rather low polymorphism, good otherwise

Yes

2055nr51

PDR1

False positive problem, weak signals

No

2055nr53

PDR1

Slight Cy3 background signal

Yes

2055 × 10

PDR1

Many signals weak or absent; Cy5 false positive problem

No

2055 × 19

PDR1

Low polymorphism, weak signals, many mixed Cy3/Cy5 signals

No

2055 × 28

PDR1

Low polymorphism, weak signals, Cy3 false positive problem

No

2055 × 29

PDR1

Many signals weak or absent; Cy5 false positive problem

No

2055 × 36

PDR1

Cy3 false positive problem

No

2201CycL6

PDR1

Rather low polymorphism

Yes

2385 × 16

PDR1

Very low polymorphism, mixed Cy3/Cy5 signals, Cy3 false positive problem

No

2385 × 23

PDR1

Rather low polymorphism

Yes

2385 × 46

PDR1

Very weak signals, Cy5 false positive problem

No

2385 × 56

PDR1

Very weak signals, Cy3/Cy5 false positive problem

No

2385 × 64

PDR1

Rather low polymorphism

Yes

2539 × 7

PDR1

Some Cy5 contaminating signal

Yes

3150 × 11

PDR1

Almost no polymorphism

No

Birte-B1

PDR1

Good

Yes

Birte-x5

PDR1

Very low polymorphism, many very weak signals

No

Birte-x16

PDR1

Good

Yes

Birte-x28

PDR1

Some weak or mixed Cy3/Cy5 scores

Yes

Birte-x34

PDR1

Good

Yes

MKRBIP2

PDR1

Slight Cy5 contamination problem

Yes

MKRBIP3

PDR1

Many missing scores

No

MKRBIP7

PDR1

Good

Yes

Cycl1074-L12

Cyclops

Some Cy5 contaminating signal

Yes

Cycl1074-L29

Cyclops

Good

Yes

Cycl711-L12

Cyclops

Many missing scores, many mixed Cy3/Cy5 scores

No

UniTpv

Tpv1

Good

Yes

DBAP-261 × 1

Indel

Very Low polymorphism

No

DBAP-2055nr53

Indel

Very Low polymorphism

No