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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.