Skip to main content

Table 1 HMPR and MSLL libraries, and alignment to 16,861 BACs.

From: Methylation-sensitive linking libraries enhance gene-enriched sequencing of complex genomes and map DNA methylation domains

Library Data

BAC Alignment Data

HMPR

ZMMB1

Library2

Enzyme

Digestion

Reads

Paired Hits

Avg Span (kb)

Avg %

Masked 3

Ha

HpyCH4 IV

10 U/ug

171

27

3.1

28%

Hb

HpyCH4 IV

0.1 U/ug

181

26

2.7

19%

Hc

HpaII

10 U/ug

734

120

3.5

28%

Hd

HpaII

0.5 U/ug

1482

278

3.5

25%

He

HpaII

0.25 U/ug

5189

913

3.3

27%

Hf

HpaII

0.125 U/ug

10428

1838

3.1

25%

Hg

HpaII

0.05 U/ug

1488

246

3.2

27%

Hh

HpaII

0.025 U/ug

177

19

3.1

19%

Hi

HpaII

0.0125 U/ug

174

22

2.6

18%

Hj

HpaII

0.005 U/ug

177

34

2.9

38%

Hk

HpaII

0.00125 U/ug

183

29

2.4

37%

Hl

HpyCH4 IV

0.5 U/ug

1441

112

2.2

31%

Hm

HpyCH4 IV

0.25 U/ug

2239

239

3.0

36%

Hn

HpyCH4 IV

0.125 U/ug

1492

239

3.0

34%

Ho

HpyCH4 IV

0.05 U/ug

2550

492

1.9

21%

Hp

HpyCH4 IV

0.025 U/ug

8218

1483

3.0

22%

Hq

HpyCH4 IV

0.0125 U/ug

1782

329

2.9

25%

Hr

HpyCH4 IV

0.005 U/ug

1544

262

2.3

23%

Hs

HpyCH4 IV

0.002 U/ug

649

115

2.3

29%

Total

  

40299

6865

3.0

26%

MSLL

ZMMB1

Library

Enzyme

Length (kb)

Reads

Paired hits

Avg Span (kb)

Avg %

Masked3

La

SalI

35–60

7536

93

46

78%

Lb

HpaII

35–60

8733

146

39

82%

Lc

HpaII

20–35

9639

483

26

78%

Ld

SalI

20–35

10916

469

24

56%

Le

HpaII

12–20

8920

630

15

65%

Lf

SalI

60–100

5436

10

80

78%

Lh

SalI

>100

6158

0

n/a

n/a

Li

HpaII

60–100

8495

21

70

86%

Lj

HpaII

>100

7715

0

n/a

n/a

Lz

HpaII

7–12

7184

807

11

55%

Total – Hpa

  

50,686

2087

 

66%

Total – Sal

  

30,046

572

 

60%

Total

  

80,732

2659

 

65%

  1. 1 The ZMMB libraries followed by the indicated suffix (e.g. ZMMBLj) can be ordered from the Arizona Genomics Institute [43].
  2. 2 HMPR clones have size ranges of 2–4 kb.
  3. 3 The percent of sequence masked within the spanned BAC regions, as determined by RepeatMasker against the TIGR maize repeat database.