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Table 1 Distribution of sequence reads in elongating cotton fiber small RNA libraries

From: Genome-wide analysis of small RNAs reveals eight fiber elongation-related and 257 novel microRNAs in elongating cotton fiber cells

RNA class

Total reads

Unique reads

 

5 dpa

10 dpa

15 dpa

20 dpa

5 dpa

10 dpa

15 dpa

20 dpa

Clean reads

17,979,849

18,747,051

19,597,538

17,845,500

7,335,047

7,111,913

6,491,658

4,878,094

Match genomea

4,983,316

7,113,695

7,107,883

8,871,116

1,828,847

1,876,311

1,731,526

1,299,290

Protein-coding genesa

198,666

175,439

189,071

160,087

82,988

90,480

112,705

101,770

Known miRNAsb

307,112

641,621

553,022

419,974

803

942

909

809

Repeatsa

467,372

509,173

454,975

441,256

197,195

182,749

162,696

125,578

rRNAa

395,288

992,921

1,363,365

2,212,532

14,564

22,415

26,009

33,079

tRNAa

174,510

1,106,240

1,104,728

2,040,671

2,418

3,772

4,456

6,779

snRNAa

1,487

2,743

3,654

5,026

585

940

1,111

1,288

snoRNAa

301

511

629

540

187

267

302

256

Othersc

16,435,113

15,318,403

15,928,094

12,565,414

7,036,307

6,810,348

6,183,470

4,608,535

  1. aBased on the G. raimondii whole genome sequence (http://cgp.genomics.org.cn/page/species/index.jsp);
  2. bThe number of reads includes the defined mature miRNAs and their 2-nt mismatch variants;
  3. cContains all of the unclassified reads that potentially include new miRNAs.
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BMC Genomics

ISSN: 1471-2164

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