Table 1

SFP detection among three varieties of cultivated tomato and sequence validation

Stringency of confidence interval

Validation rate1

No. of SFPs

Total2


FL7600 vs. OH9242

FL7600 vs. PI114490

OH9242 vs. PI114490


α ≤ 10-2

60%

3467 (2080)3

3725 (2235)

3585 (2151)

8518 (5111)

α ≤ 10-3

63%

1023 (644)

1493 (941)

1336 (842)

2970 (1871)

α ≤ 10-4

71%

435 (309)

823 (584)

736 (523)

1481 (1052)

α ≤ 10-5

74%

217 (161)

523 (387)

490 (363)

885 (655)

α ≤ 10-6

76%

135 (103)

402 (306)

336 (255)

629 (478)

α ≤ 10-7

75%

95 (71)

284 (213)

263 (197)

458 (344)


1Validation rate was calculated based on the sequence data for 189 putative SFPs

2Number of SFPs across all three two-way comparisons without redundancy

3 Number in parenthesis indicates the number of SFPs corrected by the corresponding validation rate

Sim et al. BMC Genomics 2009 10:466   doi:10.1186/1471-2164-10-466

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