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Table 2 Summary of pyrosequencing confirmation, arbitrary probes.

From: Identification of SNPs and INDELS in swine transcribed sequences using short oligonucleotide microarrays

Probe Set ID

Probe No.

Gene Name

SNP

SNP type

SNP location

Estimate

q-value

Rank q < 0.05

Rank q < 0.05, fold change > 2

Ssc.14003.2.S1_at

9

RPS4X

R, Y

Transition

15, 19

-5.09342

9.90E-35

1

1

Ssc.14343.1.S1_at

2

TPT1

Y

Transition

10

-3.66704

8.02E-32

2

2

Ssc.1341.1.S1_at

8

TKT

Y

Transition

13

-3.05487

4.13E-29

3

3

Ssc.16710.1.S1_at

4

Q9BTR0

T/-

INDEL

7

-3.07201

1.67E-26

9

9

Ssc.11554.1.S1_at

11

MRPL39

TAAG/----

INDEL

17

-3.13603

4.80E-26

10

10

Ssc.2756.1.A1_at

10

MRPL22

Y

Transition

20

-3.28928

6.28E-25

15

15

Ssc.20986.2.S1_at

4

GRN

R

Transition

13

-3.23164

1.66E-24

20

20

Ssc.24770.1.S1_at

3

PLAGL1

Y

Transition

14

-1.23548

6.85E-19

61

61

Ssc.4324.2.A1_at

4

CAMLG

S

Transversion

6

-1.8121

4.49E-15

124

124

Ssc.55.1.S1_at

9

EGFR

Y

Transition

10

-1.5839

3.27E-14

154

154

Ssc.422.1.S1_at

10

IGF2R

W

Transition

21

-1.41267

1.60E-11

259

253

Ssc.21595.2.S1_at

5

GNAS

R

Transition

19

-1.59188

2.45E-09

401

371

Ssc.2315.1.A1_at

11

Q8N3R3

S

Transversion

8

-1.77102

3.35E-08

521

447

Ssc.26344.1.S1_at

11

PAK3

R

Transition

9

-1.12922

6.41E-08

561

474

Ssc.21857.1.S1_at

11

GRB10

R

Transition

5

-0.88725

7.90E-08

576

no rank

Ssc.6989.1.A1_at

5

SFXN1

Y

Transition

17

-1.33493

1.75E-07

627

509

Ssc.939.1.A1_at

7

RPL12

K

Transversion

20

-3.21892

1.86E-07

637

514

Ssc.26344.1.S1_at

4

PAK3

None

None

 

1.068089

2.30E-07

655

523

Ssc.12365.1.A1_at

11

ADAMTS1

Y

Transition

5

-1.13449

0.000135

1345

718

Ssc.13476.1.A1_at

1

PEG10

R

Transition

10

-1.94654

0.000221

1444

732

Ssc.2716.1.A1_at

6

NP_055322

None

None

 

-1.39706

0.000241

1472

736

Ssc.7604.2.A1_a_at

11

C14orf111

M

Transversion

16

-1.52629

0.000994

1871

783

Ssc.1595.1.S1_at

1

PHEMX

None

None

 

0.973961

0.001016

1884

no rank

Ssc.26460.1.A1_at

1

SNRPN

None

None

 

-0.66999

0.00147

2003

no rank

Ssc.11508.1.A1_at

7

GABRA5

None

None

 

0.473879

0.00433

2450

no rank

Ssc.3850.1.S1_at

11

NNAT

None

None

 

-1.00118

0.008733

2860

822

Ssc.3802.1.S1_at

2

NAP1L4

A/-

INDEL

6

-0.59859

0.02431

3704

no rank

  1. Twenty-seven putative SFPs were selected, and were pyrosequenced to confirm or disprove predicted SNPs at probe locations. The column labeled 'SFP' describes the character of the polymorphism discovered, such as transitions/transversions, INDELs (MRPL39, NAP1L4), or false positives ("None"). When filtering out probes with less than 2-fold expression difference between breeds, 87% of predicted SNPs were true.
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BMC Genomics

ISSN: 1471-2164

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