Using paired-end sequences to optimise parameters for alignment of sequence reads against related genomes

BMC Genomics

Table 3 Calculation of true and false positive and false negative rates from search results.

Score cut-off¹	BESs with positions	BESs in tail-to-tail BACs	BESs predicted to be in tail-to-tail BACs²	fp rate³	fn rate⁴
8	292,916	130,358	230,616	0.43	0.21
40	283,315	130,236	215,746	0.40	0.24
45	263,060	129,806	186,000	0.30	0.30
50	245,983	128,826	162,636	0.21	0.34
55	236,647	126,698	150,524	0.16	0.36
60	231,047	125,670	143,484	0.12	0.38
65	225,201	123,140	136,314	0.10	0.40
70	221,398	121,134	131,750	0.08	0.40
100	200,409	106,368	107,954	0.01	0.46

¹results from the MegaBLAST search on full length BESs using a contiguous word size of 8 the default score cut-off is 8, the results in this row correspond to the case where no score cut-off is specified.
²for each score cut-off the number of BESs predicted to be in tail-to-tail BACs assuming all BESs were correctly positioned.
³false positive rate
⁴false negative rate

ISSN: 1471-2164