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Table 5 Comparison of repetitive elements

From: Comparative genomic analysis of human infective Trypanosoma cruzi lineages with the bat-restricted subspecies T. cruzi marinkellei

 

T. c. marinkellei

T. c. cruzi Sylvio X10

 

Element

# bpa

% Short readsb

# bpa

% Short readsb

SEc

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%

 
  1. a The sum of masked base pairs in the assembly. The number inside parenthesis refers to the percentage of assembled bases.
  2. b The percentage of short reads that was mapped on these features.
  3. 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.