Table 1.

Summary of mobile element insertion prediction results in the Venter genome

Chromosome	Validated	Predicted	Found	Recall (%)	Precision (%)
Chromosome 1	41 Alu	42 Alu	40	88	95
	4 NCAI
Chromosome 2	59 Alu	57 Alu	56	91	98
	2 NCAI
Chromosome 3	42 Alu	40 Alu	40	90	100
	1 NCAI
	1 SVA
Chromosome 4	43 Alu	41 Alu	40	87	97
	4 NCAI	1 NCAI	1
Chromosome 5	39 Alu	44 Alu	35	90	80
	1 SVA	1 SVA	1
Chromosome 6	59 Alu	55 Alu	53	88	96
	1 NCAI
	1 SVA	1 SVA	1
Chromosome 7	24 Alu	22 Alu	20	83	91
Chromosome 8	34 Alu	33 Alu	33	92	100
	2 NCAI
Chromosome 9	23 Alu	23 Alu	21	88	92
	1 NCAI	1 NCAI	1
	1 SVA
Chromosome 10	33 Alu	32 Alu	32	94	100
	2 NCAI	1 NCAI	1
Chromosome 11	35 Alu	32 Alu	32	85	100
	3 NCAI	1 NCAI	1
	2 SVA	1 SVA	1
Chromosome 12	33 Alu	34 Alu	31	84	91
	4 NCAI
Chromosome 13	34 Alu	34 Alu	34	90	100
	3 NCAI
	2 SVA	1 SVA	1
Chromosome 14	19 Alu	20 Alu	19	95	95
	1 NCAI
	2 SVA	2 SVA	2
Chromosome 15	24 Alu	21 Alu	20	83	95
Chromosome 16	12 Alu	12 Alu	12	80	100
	3 NCAI	1 NCAI	1
Chromosome 17	9 Alu	9 Alu	9	77	100
	2 NCAI
	2 SVA	1 SVA	1
Chromosome 18	22 Alu	21 Alu	20	91	95
Chromosome 19	11 Alu	11 Alu	11	80	100
	3 NCAI	1 NCAI	1
	1 SVA
Chromosome 20	11 Alu	13 Alu	9	77	71
	2 NCAI	1 NCAI	1
Chromosome 21	7 Alu	7 Alu	7	100	100
Chromosome 22	7 Alu	5 Alu	5	71	100

We show the precision and recall rates of our mobile element (Alu, NCAI and SVA) insertion discovery. We compare our mobile element insertion predictions with both (Xing et al., 2009) and the HuRef genome assembly (Levy et al., 2007). The results demonstrate that our algorithm has a high recall and precision rate.