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Table 1 Locations of unplaced scaffolds on GRCm38/mm10 a

From: BAIT: Organizing genomes and mapping rearrangements in single cells

Accession numberb

Scaffold size, kb

Localizes to: ,Mbb

Strand directionb

% Concc

Librariesc, n

Gapsd

Gap locatione

(u), n

(b), n

Primary

Alternate

GL456382.1

23.2

chrX:0–57.6

+

100

18

14

26

  

GL456379.1

72.4

chrX:0–57.6

-

97.8

46

14

26

  

GL456233.1

336.9

chrX:0–57.6

-

96.1

51

14

26

  

JH584299.1

953.0

chr5:90.4-96.6

+

94.2

52

0

1

chr5:94,088,336-94,138,335

 

GL456239.1

40.1

chr1:0–12.6

-

91.1

56

3

1

chr1:0–3,000,000

 

GL456367.1

42.1

chrX:0–57.6

-

90.0

40

14

26

  

GL456381.1

25.9

chrX:0–57.6

-

90.0

50

14

26

  

GL456393.1

55.7

chr3:28.6-31.6

+

89.3

56

0

0

chr3:40,550,618-40,650,617

 

GL456359.1

23.0

chr4:136.4-156.2

-

88.7

53

1

19

chr4:156,408,117-156,508,116

chr4:130,393,226-130,516,309

GL456354.1

196.0

chr5:90.4-100.6

-

88.6

35

0

1

chr5:94,088,336-94,138,335

 

GL456385.1

35.2

chr13:0–6.8

-

87.3

55

3

0

chr13:1–3,000,000

 

GL456360.1

31.7

chr15:88.4-103.8

+

87.0

54

1

3

chr15:103,943,686-104,043,685

 

GL456366.1

47.1

chr15:62.4-103.8

+

85.5

55

1

3

chr15:103,943,686-104,043,685

 

GL456216.1

66.7

chr4:136.4-156.2

+

80.4

51

2

19

chr4:156,408,117-156,508,116

chr4:130,393,226-130,516,309

JH584296.1

199.4

chr5:83.6-113.2

-

80.0

10

1

1

chr5:113,521,975-113,535,974

 

JH584297.1

205.8

chr5:88.6-100.6

-

77.8

18

0

1

chr5:94,088,336-94,138,335

 

GL456368.1

20.2

chr4:129.2-156.2

-

76.2

42

2

19

chr4:130,393,226-130,516,309

chr4:156,408,117-156,508,116

GL456221.1

207.0

chr1:79.8-123.2

+

73.7

57

2

4

chr1:85,347,104-85,447,103

chr1:75,055,557-75,121,556

GL456392.1

23.6

chr2:0–8.2

-

73.5

34

4

0

chr2:0–3,050,000

 

JH584292.1

14.9

chr4:107.8-108.6

+

73.5

49

0

1

chr4:99,842,111-99,876,234

 

GL456372.1

28.7

chr1:127.2-146.2

-

69.2

52

1

1

chr1:156,118,744-156,168,743

 

GL456389.1

28.8

chrX:0–57.6

-

63.6

33

14

26

  

GL456370.1

26.8

chr4:67.6-68.8

-

62.0

50

0

3

chr4:61,344,177-61,394,176

 
  1. aOf the 44 orphan scaffolds, 23 had enough reads to determine their genomic location by calculating mapping concordance.
  2. bThe scaffold accession numbers and BAIT-determined locations are given, together with the strand direction, which gives the relative orientation of the scaffolds with respect to the genome.
  3. cThe percentage concordance (% conc) and the number of libraries with enough information to make a concordance call are also given.
  4. dFinally, BAIT cross-referenced these locations to unbridged and bridged gaps falling over the interval (gap (u) and gap (b) respectively.
  5. ePrimary and alternate gap locations are given. To ensure no regions were missed, gaps were included within 10 Mb away from the determined interval.
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Genome Medicine

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