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Table 1 Comparison of STRScan and lobSTR on STR identification from shotgun sequencing reads

From: STRScan: targeted profiling of short tandem repeats in whole-genome sequencing data

STR markers

Chromosome / location

# in reference genome

Copy number of identified STRs (number of supporting reads)

   

Venter

HG00145

HG00140

   

STRScan

lobSTR

STRScan

lobSTR

STRScan

lobSTR

YSTR (on Y chromosome) panel

DYS19

chrY 9521989-9522052

15

14(1)

-

-

-

-

-

DYS385a

chrY 20801599-20801642

11

11(2)

11(1)

11(3)

-

12(1)

-

 

chrY 20842518-20842573

14

14(1)

14(1)

    

DYS388

chrY 14747535-14747570

12

12(2)

12(1)

-

-

-

-

DYS389I

chrY 14612242-14612289

12

13(3)

13(1)

-

-

-

-

DYS389II

chrY 14612242-14612405

29

29(2)

29(2)

-

-

-

-

DYS390

chrY 17274947-17275042

24

23(1)

23(1)

15(1)

-

-

-

DYS391

chrY 14102795-14102838

11

10(1)

10(1)

-

-

10(2)

10(2)

DYS392

chrY 22633873-22633911

13

13(2)

13(2)

-

-

  

DYS393

chrY 3131152-3131199

12

13(2)

-

-

-

-

-

DYS426

chrY 19134850-19134885

12

12(1)

12(1)

-

-

-

-

DYS437

chrY 14466994-14467057

16

-

-

-

-

16(2)

-

DYS438

chrY 14937824-14937873

10

12(1)

12(1)

-

-

10(1)

10(1)

DYS439

chrY 14515312-14515363

13

12(1)

12(1)

-

-

11(1)

11(1)

DYS447

chrY 15278740-15278854

23

25(1)

-

-

-

-

-

DYS448

chrY 24365070-24365225

19

-

-

-

-

-

8(1)

DYS460 (A7.1)

chrY 21050842-21050881

10

12(2)

-

-

-

11(1)

-

H4

chrY 18743553-18743600

12

-

-

12(1)

12(1)

11(2)

-

YCAIIa

chrY 19622111-19622156

23, 23

19(3), 23(5)

19(3), 23(4)

19(1)

19(2)

-

-

 

Total

18

15(31)

11(20)

4(6)

2(3)

7(10)

4(5)

CODIS (on autosomes) panel

CSF1PO

chr5 149455887-149455938

13

11(7)

11(5)

-

-

11(1)

11(1)

D13S317a

chr13 82722160-82722203

11

12(1),13(2)

11(1)

-

-

-

-

D16S539

chr16 86386308-86386351

11

12(2)

-

13(1)

-

11(2)

11(1)

D18S51

chr18 60948900-60948971

18

14(2)

14(2)

-

-

15(1)

-

D21S11

chr21 20554291-20554417

29

-

-

-

-

-

-

D3S1358a

chr3 45582231-45582294

16

16(3)

16(3)

-

-

-

-

D5S818

chr5 123111250-123111293

11

-

-

-

-

-

-

D7S820

chr7 83789542-83789593

13

10(3)

10(2)

-

-

8(3)

-

D8S1179

chr8 125907107-125907158

13

12(1)

12(1)

8(1)

6(2)

-

13(1)

FGAa

chr4 155508888-155508975

22

26(1), 21(1)

26(1), 21(1)

-

-

-

-

PentaD

chr21 45056086-45056150

13

13(2)

-

9(1)

9(1)

-

-

PentaE

chr15 97374245-97374269

5

12(2)

12(1)

-

-

13(1)

13(1)

TH01

chr11 2192318-2192345

7

6(2)

-

-

-

5(1),10(2)

10(2)

TPOX

chr2 1493425-1493456

8

8(5)

8(4)

-

-

8(1)

8(1)

 

Total

14

12(34)

9(21)

3(3)

2(4)

7(12)

6(7)

  1. aMulti-allelic STR markers, each with two alleles on the reference human genome