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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