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Table 2 Details on the types of mis-assemblies and feature characteristics for the results presented in Table 1

From: Genome assembly forensics: finding the elusive mis-assembly

   Mis-assembly types Mis-assembly signatures Suspicious regions
Species Len Ins Del Join Inv Num aLen %Len Num aLen %Len
B. anthracis 5.2 0 0 2 0 1,336 831 21.5 127 5,546 13.6
B. suis 3.4 0 0 7 3 1,047 1,354 42.2 158 7,575 35.6
C. burnetii 2.0 0 0 13 9 1,375 1,106 74.3 124 11,455 69.4
C. caviae 1.4 0 0 11 1 625 320 14.1 50 3,896 13.7
C. jejuni 1.8 1 0 3 1 290 613 10.0 61 1,981 6.8
D. ethenogenes 1.8 0 0 8 4 688 691 26.5 88 4,116 20.2
F. succinogenes 4.0 0 1 19 1 1,670 1,387 57.5 266 7,396 48.8
L. monocytogenes 2.9 0 0 1 0 1,381 873 42.1 201 5,254 36.9
M. capricolum 1.0 3 0 0 0 83 835 6.8 16 3,005 4.7
N. sennetsu 0.9 0 0 0 0 91 512 5.4 13 2,328 3.5
P. intermedia 2.7 0 0 19 2 1,655 727 44.5 201 6,263 46.5
P. syringae 6.4 0 1 43 20 2,841 782 34.4 366 5,725 32.4
S. agalactiae 2.1 0 0 16 5 687 793 25.6 112 4,082 21.5
S. aureus 2.8 1 0 34 6 1,850 740 49.0 227 5,582 45.4
W. pipientis 3.3 0 0 17 14 761 1,206 28.1 132 6,395 25.8
X. oryzae 5.0 1 0 74 76 2,569 1,551 79.0 100 27,771 55.1
Totals 46.8 6 2 267 142 18,949 895 35.1 2242 6773 30.0
  1. Phrap mis-assemblies are grouped into tandem insertion (Ins), tandem collapse (Del), mis-join (Join), and inversion (Inv) events in columns 3-6. Columns 7-9 give the total count (Num), average length (aLen), and total length as a percentage of genome (%Len) for the amosvalidate mis-assembly signatures. Columns 10-12 give the same information, but for amosvalidate suspicious regions.