Detection of genome-wide polymorphisms in the AT-rich Plasmodium falciparum genome using a high-density microarray

Table 3 Summary of mSFP calls for the 14 chromosomes among five parasite isolates

Isolate	Ch1	Ch2	Ch3	Ch4	Ch5	Ch6	Ch7	Ch8	Ch9	Ch10	Ch11	Ch12	Ch13	Ch14	Total
0000*	35727	54790	67238	67463	90602	85998	85713	86826	98064	190050	223105	212037	340227	231400	1869240
0001	247	615	656	896	429	506	655	524	635	765	606	1092	1486	1337	10449
0010	209	116	130	331	304	211	252	313	1529	54	390	245	393	244	5121
0011	180	41	49	244	55	137	143	269	121	173	98	165	156	76	1907
0100	349	1636	348	688	537	344	683	527	497	761	829	1224	890	755	10068
0101	248	556	73	479	279	203	336	268	193	191	178	315	164	137	3620
0110	175	165	193	491	173	267	384	199	227	506	223	488	478	222	4191
0111	296	213	235	551	941	501	406	513	389	543	378	866	597	397	6826
1000	300	278	359	563	345	467	580	598	511	1125	687	762	1287	994	8856
1001	138	241	123	427	138	401	625	315	315	621	484	342	490	327	4987
1010	179	75	70	219	55	81	117	136	49	182	275	106	209	162	1915
1011	243	288	144	533	47	593	447	438	369	363	282	348	684	316	5095
1100	123	179	166	309	87	141	343	143	78	204	177	272	424	142	2788
1101	477	271	356	860	240	1180	134	495	356	496	476	880	547	207	7975
1110	363	197	340	731	222	306	628	433	133	408	402	560	644	222	5589
1111	2507	1924	1607	3829	968	3720	4215	3149	2816	3984	3072	3948	3809	2152	41700
Total	6034	6795	4849	11151	4820	9058	10948	8320	8218	10776	8557	11613	12258	7690	121087

*Parasite isolate order is 7G8, Dd2, FCR3, and HB3. For example, '1000' indicates the numbers of unique alleles for 7G8. A '0' indicates that a parasite has the same allele as that of 3D7 (0), and '1' indicates a different allele (a mSFP). The numbers in the first row were positions with probes but no SFP were called (no polymorphism). These numbers were not counted in the total calculation. The counts were based on a signal cutoff value of 5.0. Note these calls were mSFP and were different from those defined previously, where each probe was defined as an independent SFP[28].

ISSN: 1471-2164