Table 5

Comparison of repetitive elements
T. c. marinkellei T. c. cruzi Sylvio X10
Element # bp a % Short reads b # bp a % Short reads b SE c
VIPER 574,697 (1.679 %) 1.535 1,116,378 (2.892 %) 1.811 Tcc X10
DIRE 433,619 (1.267 %) 1.156 655,064 (1.697 %) 0.907 Tcm
L1Tc 432,474 (1.263 %) 1.168 805,885 (2.088 %) 2.158 Tcc X10
TcTREZO 382,416 (1.117 %) 1.024 481,685 (1.248 %) 1.081 Tcc X10
E22 223,679 (0.653 %) 0.630 281,491 (0.729 %) 0.590 Tcc X10
SIRE 176,724 (0.516 %) 0.497 238,914 (0.619 %) 0.527 Tcc X10
SZ23 94,765 (0.277 %) 0.224 151,879 (0.393 %) 0.275 Tcc X10
CZAR 18,338 (0.054 %) 0.104 102,810 (0.266 %) 0.203 Tcc X10
NARTc 4,705 (0.014 %) 0.010 10,936 (0.028 %) 0.020 Tcm
C6 2,944 (0.009 %) 0.006 167 (0.000 %) 0.000 Tcm
TCSAT1 621 (0.002 %) 0.149 7,573 (0.020 %) 0.628 Tcc X10
Total 2,344,982 (6.851%) 6.503% 3,852,782 (9.98%) 8.200%

a The sum of masked base pairs in the assembly. The number inside parenthesis refers to the percentage of assembled bases.

b The percentage of short reads that was mapped on these features.

c SE=Significantly Enriched. Refers to if one genome contained significantly more of this gene family. The significance was determined from an empirical distribution of read depth differences from homologous regions of Tcm and Tcc X10, corrected for genome size. The empirical distribution was used to calculate a p-value.

Franzén et al.

Franzén et al. BMC Genomics 2012 13:531   doi:10.1186/1471-2164-13-531

Open Data