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Table 4 Calculation of the amount of LOH in BT-474

From: Whole genome sequence analysis of BT-474 using complete Genomics’ standard and long fragment read technologies

Chromosome

Base pairs

Variations

Centromere position (Mbp)

% LOH

LOH (bp)

LOH (variations)

1

249,250,621

4,401,091

125

0.0 %

0

0

2

243,199,373

4,607,702

93.3

0.0 %

0

0

3

198,022,430

3,894,345

91

40.4 %

80000000

1573295

4

191,154,276

3,673,892

50.4

0.0 %

0

0

5

180,915,260

3,436,667

48.4

0.0 %

0

0

6

171,115,067

3,360,890

61

0.0 %

0

0

7

159,138,663

3,045,992

59.9

0.0 %

0

0

8

146,364,022

2,890,692

45.6

34.2 %

50000000

987501

9

141,213,431

2,581,827

49

24.8 %

35000000

639910

10

135,534,747

2,609,802

40.2

41.0 %

55534747

1069355

11

135,006,516

2,607,254

53.7

40.7 %

55006516

1062289

12

133,851,895

2,482,194

35.8

0.0 %

0

0

13

115,169,878

1,814,242

17.9

100.0 %

115169878

1814242

14

107,349,540

1,712,799

17.6

0.0 %

0

0

15

102,531,392

1,577,346

19

75.0 %

76898544

1183010

16

90,354,753

1,747,136

36.6

0.0 %

0

0

17

81,195,210

1,491,841

24

0.0 %

0

0

18

78,077,248

1,448,602

17.2

0.0 %

0

0

19

59,128,983

1,171,356

26.5

0.0 %

0

0

20

63,025,520

1,206,753

27.5

0.0 %

0

0

21

48,129,895

787,784

13.2

0.0 %

0

0

22

51,304,566

745,778

14.7

100.0 %

51304566

745778

X

155,270,560

2,174,952

60.6

100.0 %

155270560

2174952

Total

3,036,303,846

55,470,937

1,028

 

674,184,811

11,250,331

% of total in LOH

    

22.2 %

20.3 %

  1. Loss of heterozygosity (LOH) in the genome of BT-474 was calculated based on the genomic distance covered by large areas (>10 mb), where the lesser allele fraction is zero. In our data the lesser allele was calculated in 100 kb windows, based on read counts at all fully called variant loci. An explanation of the fields are as follows: chromosome, the chromosome for which each LOH region was calculated; base pairs, the total number of base pairs for each chromosome based on the NCBI reference genome build 37; variations, total number of confirmed variations for each chromosome based on Ensembl genome browser release 68; centromere position (Mbp), the location in megabases of the centromere for each chromosome; %LOH, the percentage of each chromosome estimated to have LOH; LOH (bp), the total number of base pairs for each chromosome that are estimated to be found in LOH regions; the total number of variations from Ensembl genome browser release 68 that are found within the estimated LOH region