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Table 3 Repeat content of haplotype assemblies. Repeat masking is performed using the rodentia repeat library and RepeatMasker

From: A haplotype-resolved genome assembly of the Nile rat facilitates exploration of the genetic basis of diabetes

Repeat

Paternal

 

Maternal

 
 

Number of elements

Percent genome

Number of elements

Percent genome

SINE

1097531

6.02

1095360

6.03

Alu/B1

449074

1.98

447915

1.98

B2-B4

584908

3.81

583853

3.82

IDs

34995

0.1

34992

0.1

MIRs

27964

0.13

28010

0.13

LINEs:

489920

12.26

488452

12.21

LINE1

474324

12.15

472927

12.11

LINE2

11535

0.08

11496

0.08

L3/CR1

2636

0.02

2598

0.02

LTR

801475

11.23

797822

11.18

ERVL

70619

0.89

70801

0.9

ERVL-MaLRs

355720

3.96

355437

3.99

ERV_classI

53595

0.8

52958

0.8

ERV_classII

318728

5.55

315822

5.48

Satellite

59080

0.28

58663

0.28

Simple repeat

1289416

2.76

1284006

2.75

Low complexity

149866

0.39

149072

0.39

Total (including other)

34.4

 

34.32