Accurate measurement of gene copy number for human alpha-defensin DEFA1A3

BMC Genomics

Table 1 Examples of integer copy number inference from PRT and ratio data

Sample ID	MLCN	Minimum ratio (MR)	MLT1A0 PRT	DEFA4 PRT	indel5 ratio	indel5 integers	DefHae3 ratio	DefHae3 integers	7bpdup ratio	7bpdup integers
NA12751	7	511.47	7.07	7.03	1.32	4:3	2.38	5:2	0.41	2:5
C0052	8	152.11	8.30	7.70	1.07	4:4	5.66	7:1	0.60	3:5
NA12749	5	21.99	5.71	5.21	(No data)	-	3.70	4:1	3.74	4:1
C0157	9	10.50	9.09	9.02	1.18	5:4	6.12	8:1	0.78	4:5
NA12778	6	3.26	(No data)	7.59	1.12	3:3	5.49	5:1	0.21	1:5

Examples of copy number inference from PRT and ratio data. For each sample the table shows the MLCN (maximum likelihood copy number) derived by combining information from different measures (see text and Table 2) and the minimum ratio (MR) score indicating the confidence with which that copy number is assigned. For the three ratio tests (indel5, DefHae3 and 7bpdup), the measured ratio is shown alongside the integer interpretation derived from the MLCN that best fits the observed ratio. Samples are arranged in decreasing order of confidence, as reflected in decreasing values of the minimum ratio (MR).

ISSN: 1471-2164