Table 4

Mean allele balances of heterozygous SNVs genome-wide and in CTRs

Control I

Additional samples

Exome capture method

Number of samples

Genome-wide^a

CTR^b

Genome-wide^a

CTR^b

Student's t-test P^c

Agilent SureSelect

3

0.517

0.524

0.511

0.517

0.007

Agilent SureSelect 50 Mb

3

0.515

0.520

0.514

0.519

0.003

NimbleGen SeqCap

20

0.516

0.527

0.514

0.523

7.1 × 10^-15

NimbleGen SeqCap v2.0

3

0.512

0.518

0.514

0.519

0.013

^aAll called heterozygous SNVs with minimum sequencing coverage of 20×, regardless of target region. ^bHeterozygous SNVs with minimum sequencing coverage of 20× called within the CTRs. ^cStudent's t-test P-value for the difference between CTR and all sequenced regions given for the combined sample set of the control I sample and 25 additional samples.

Sulonen et al. Genome Biology 2011 12:R94   doi:10.1186/gb-2011-12-9-r94