TABLE 6.

Verification of TSC trace predictions by PCR

dbSNP no.	Chromosomal locationa	Type of transposon	Alleles examined	% golden path allele	% trace allele
ss8475858	Chr1: 35,902,357–35,902,357b	Alu Ya5	48	4	96
ss8475874	Chr1: 43,270,765–43,271,100	Alu Y	46	11	89
ss8476214	Chr1: 180,191,288–180,191,688	Alu Yg6	46	46	54
ss8480173	Chr2: 184,452,525–184,452,867	Alu Ya5	46	4	96
ss8481265	Chr3: 117,596,173–117,596,496	Alu Ye5	44	0	100
ss8481475	Chr3: 182,282,816–182,283,143	Alu Y	16	63	38
ss8481677	Chr4: 36,367,085–36,367,417	Alu Ya4	20	30	70
ss8481874	Chr4: 98,569,039–98,569,364	Alu Ya5	44	43	57
ss8481886	Chr4: 100,528,683–100,528,998	Alu Ya5	48	0	100
ss8481943	Chr4: 127,436,762–127,437,090	Alu Ya4	44	11	89
ss8482744	Chr5: 174,741,730–174,742,046	Alu Y	14	21	79
ss8482858	Chr6: 20,873,358–20,873,677	Alu Ya5	32	44	56
ss8482986	Chr6: 52,830,475–52,830,475	Alu Y	48	96	4
ss8483054	Chr6: 74,416,861–74,417,166	Alu Ya5	36	14	86
ss8483191	Chr6: 116,796,384–116,796,702	Alu Yi6	14	14	86
ss8483704	Chr7: 94,998,283–94,998,613	Alu Ya4	32	22	78
ss8484187	Chr8: 76,176,865–76,177,188	Alu Ya5	48	40	60
ss8484397	Chr8: 140,446,315–140,446,646	Alu Yg6	48	4	96
ss8484534	Chr9: 30,481,284–30,481,594	Alu Ya5	44	20	80
ss8484574	Chr9: 41,460,809–41,461,130	Alu Ya5	46	2	98
ss8484611	Chr9: 74,581,632–74,581,947	Alu Yb8	48	33	67
ss8476640	Chr10: 53,785,800–53,786,116	Alu Y	10	50	50
ss8477096	Chr11: 42,428,408–42,428,718	Alu Yb9	20	5	95
ss8477278	Chr11: 102,948,539–102,948,851	Alu Yd8	48	0	100
ss8477519	Chr12: 45,361,618–45,361,965	Alu Yf1	48	0	100
ss8477629	Chr12: 89,348,858–89,349,061	Alu Ya4/Ya5	48	4	96
ss8478585	Chr15: 79,108,405–79,108,719	Alu Ya5	48	29	71
ss8478989	Chr17: 13,905,127–13,905,415	Alu Y	44	9	91
ss8480426	Chr20: 11,512,266–11,512,588	Alu Sx	26	31	69
ss8480530	Chr20: 53,978,074–53,978,387	Alu Ya5	48	4	96
ss8480534	Chr20: 55,148,643–55,148,959	Alu Y	20	10	90
ss8480629	Chr21: 29,522,273–29,522,612	Alu Yb8	46	17	83
ss8484940	ChrX: 115,208,464–115,208,782	Aluc	20	60	40
ss8480093	Chr2: 160,351,662–160,354,192	L1 Ta-0	20	10	90
ss8480896	Chr3: 7,322,025–7,322,322	L1 pre TA	20	40	60
ss8480972	Chr3: 33,524,976–33,525,861	L1 Ta-1nd	20	60	40
ss8481820	Chr4: 78,694,670–78,694,935	L1 pre TA	12	33	67
ss8482149	Chr4: 182,572,693–182,574,194	L1 Ta-1	48	0	100
ss8482285	Chr5: 24,416,029–24,418,937	L1 Ta-1	18	11	89
ss8482213	Chr5: 2,021,152–2,024,339	L1 Ta-1d	20	50	50
ss8483298	Chr6: 153,060,963–153,064,780	L1 Ta-1d	20	30	70
ss8483034	Chr6: 66,255,638–66,257,631	L1 Ta-1	20	25	75
ss8483013	Chr6: 57,469,905–57,475,956	L1 PA3	48	0	100
ss8484339	Chr8: 126,551,711–126,557,723	L1 Ta-1d/Ta-0	20	75	25
ss8484350	Chr8: 129,421,743–129,427,855	L1 Ta-1d	16	6	94
ss8484672	Chr9: 96,187,490–96,188,291	L1 pre TA	18	11	89
ss8477608	Chr12: 82,346,513–82,347,076	L1 Ta-1	16	12.5	87.5
ss8477509	Chr12: 40,524,321–40,525,144	L1 Ta-1	18	22	78
ss8478229	Chr14: 49,510,268–49,510,585	L1 pre TA	20	90	10
ss8478193	Chr14: 38,088,431–38,090,252	L1 pre TA	20	60	40
ss8478558	Chr15: 68,737,658–68,743,326	L1 Ta-1d/Ta-0	20	75	25
ss8479344	Chr18: 50,014,733–50,014,733	L1 Ta	18	39	61
ss8479308	Chr18: 39,283,540–39,284,523	L1 Ta-1	20	20	80
ss8480503	Chr20: 42,710,042–42,711,239	L1 Ta-1	20	70	30
ss8481522	Chr3: 195,440,681–195,441,437	SVA	48	46	54
ss8483321	Chr6: 158,457,569–158,458,368	SVA	48	17	83
ss8483556	Chr6: 29,793,437–29,796,056	SVA	48	4	96
ss8483421	Chr7: 10,248,637–10,250,470	SVA	48	67	33
ss8483579	Chr7: 55,028,493–55,030,810	SVA	44	32	68
ss8478175	Chr14: 33,497,755–33,499,561	SVA	48	75	25
ss8477420	Chr12: 13,090,355–13,090,458	5S	48	67	33

^aChromosomal coordinates are given for the July 2003 build (build 34) of the human genome sequence (University of California, Santa Cruz; Kent et al. 2002).

^bIn cases where both chromosomal coordinates are the same, the insertion occurred in the trace.

^cToo short to classify.