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Table 2 Comparison of different gene enrichment and unfiltered methods, showing percentages of sequence masked by repeats in various categories of the TIGR v4.0 maize repeat database, as well as percentages of sequences having similarity to a maize EST contig.

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

 

MSLL-Sal

MSLL-Hpa

HMPR

MF

HC

RM

UF

Sequences1

30,046

50,686

40,299

133,806

172,600

191,715

49,364

Avg. size (bp)

671

698

932

1172

1094

337

748

Retro

20%

20%

11%

26%

12%

4%

64%

Transposon

0.6%

0.9%

0.7%

0.5%

0.7%

0.3%

0.6%

MITE

0.6%

1.3%

1.0%

0.4%

0.7%

0.6%

0.2%

Centromere

0.2%

0.9%

0.2%

0.4%

0.09%

0.02%

0.8%

Telomere

0.001%

0.03%

0.08%

0.02%

0.02%

0.02%

0.01%

Ribosomal

0.4%

1.5%

1.3%

0.2%

0.1%

0.1%

2.1%

Unknown

14%

19%

13%

9%

14%

7%

14%

Total repeat

37%

42%

28%

38%

27%

12%

82%

EST Contigs

31%

16%

22%

25%

21%

22%

7%

  1. 1 The MF, HC sequences are contigs of reads; all other types are direct reads.