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Table 3 Comparison of genome localization by retroelement lineage

From: Genomic neighborhoods for Arabidopsisretrotransposons: a role for targeted integration in the distribution of the Metaviridae

Hypotheses

Test

Group(s) tested

p-values by chromosome

Accept?

   

1

2

3

4

5

 

All families are randomly distributed according to a uniform distribution

Uniform goodness of fit, 10,000 random permutations

MV(F)

0.0000

0.0000

0.0000

0.0000

0.0000

No

  

PV(F)

0.0000

0.0007

0.0000

0.0022

0.0464

No

  

MV(S)

0.0000

0.0000

0.0000

0.0000

0.0000

No

  

PV(S)

0.0000

0.0000

0.0000

0.0000

0.0000

No

  

MV(R)

0.0000

0.0000

0.0000

0.0000

0.0000

No

  

PV(R)

0.0000

0.0007

0.0000

0.0097

0.0000

No

  

NL(R)

0.0000

0.0000

0.0000

0.0002

0.0000

No

Retroelement family distributions are organized similarly in the genome

MRPP, 10,000 random permutations

MV(FSR), PV(FSR), NL(R)

0.0000

0.0000

0.0000

0.0000

0.0000

No

  

MV(FSR), PV(FSR)

0.0000

0.0000

0.0000

0.0000

0.0000

No

  

MV(FSR), NL(R)

0.0000

0.0000

0.0000

0.0000

0.0000

No

  

PV(FSR), NL(R)

0.3498

0.8326

0.0241

0.1468

0.1417

Yes

All Metaviridae sublineages have similar distributions

MRPP, 10,000 random permutations

MV Athila, Metavirus, Tat

0.2200

0.1365

0.5676

0.4174

0.2788

Yes

  

MV Athila, Metavirus

0.1057

0.3010

0.2657

0.4526

0.4453

Yes

  

MV Athila, Tat

0.1687

0.0970

0.7116

0.3773

0.2781

Yes

  

MV Metavirus, Tat

0.4903

0.1268

0.7341

0.5753

0.2361

Yes

Metaviridae subtypes have similar distributions

MRPP, 10,000 random permutations

MV(FSR)

0.7742

0.1247

0.0000

0.7425

0.0659

Yes

  

MV(FS)

0.4544

0.1357

0.0003

0.4435

0.7241

Yes

  

MV(FR)

0.5184

0.9461

0.5750

0.5480

0.2135

Yes

  

MV(SR)

0.9068

0.1339

0.0051

0.8194

0.0157

Yes

Pseudoviridae subtypes have similar distributions

MRPP, 10,000 random permutations

PV(FSR)

0.0509

0.2039

0.2199

0.0953

0.0379

Yes

  

PV(FS)

0.2732

0.0853

0.2665

0.6567

0.0453

Yes

  

PV(FR)

0.0136

0.5055

0.1185

0.0521

0.0281

Yes

  

PV(SR)

0.0743

0.5604

0.2513

0.0307

0.3476

Yes

  1. MV, Metaviridae; PV, Pseudoviridae; NL, non-LTR retrotransposon; R, RT-only; S, solo LTR; F, full-length element. p-values < 0.05 are displayed in bold text.
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Genome Biology

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