Feature Description

SMAP compare only needs two final BED files containing loci, created with SMAP delineate.

Examples of input BED files are shown below:

Set1 contains GBS samples of 48 diploid individuals.
Set2 contains 16 replicate Pool-Seq GBS samples of those constituent 48 individuals.

Reference

Start

End

MergedCluster_name

Mean_read_depth

Strand

SMAPs

Completeness

nr_SMAPs

Name

scaffold_1

41455

41541

scaffold_1:41456-41541_+

604

+

41456,41541

8

2

48_individuals

scaffold_1

41486

41569

scaffold_1:41487-41569_-

579

-

41487,41569

3

2

48_individuals

scaffold_1

42704

42778

scaffold_1:42705-42778_+

61

+

42705,42778

2

2

48_individuals

scaffold_1

42798

42884

scaffold_1:42799-42884_-

72

-

42799,42884

2

2

48_individuals

scaffold_1

77857

77943

scaffold_1:77858-77943_+

43

+

77858,77943

3

2

48_individuals

scaffold_1

156606

156692

scaffold_1:156607-156692_-

1067

-

156607,156692

37

2

48_individuals

scaffold_12

2530

2596

scaffold_12:2531-2596_+

39

+

2531,2596

3

2

48_individuals

scaffold_12

33659

33725

scaffold_12:33660-33725_+

18

+

33660,33725

1

2

48_individuals

scaffold_12

34732

34806

scaffold_12:34733-34806_+

890

+

34733,34806

45

2

48_individuals

scaffold_12

34732

34806

scaffold_12:34733-34806_-

768

-

34733,34806

47

2

48_individuals

scaffold_34

36267

36358

scaffold_34:36268-36358_+

1169

+

36268,36296,36358

36

3

48_individuals

scaffold_34

46267

46334

scaffold_34:46268-46334_-

150

-

46268,46334

48

2

48_individuals

scaffold_72

23080

23166

scaffold_72:23081-23166_-

1423

-

23081,23156,23166

48

3

48_individuals