Table 1.

Numbers of loci during the stepwise construction of the microhaplotypes (MHs) panel.

Chr	Length ≤ 80 & SNP ≥ 2	Ae a ≥ 3	Ae ≥ 4	MHs with the Largest Ae from All Overlapping Sequences in Each Group	Remove the MHs with Obvious Repeat Motifs in the Base Sequence	MHs with Physical Position ≥ 10 Mb as an Interval	MHs with Successful Primer Design	MHs Retained after Six Rounds of Optimization
1	381,886	4969	781	177	150	16	12	5
2	395,095	3944	493	139	118	17	13	5
3	332,581	3286	373	93	79	10	6	1
4	374,323	5527	1038	186	172	11	8	5
5	295,470	3066	305	98	88	10	8	3
6	411,469	19,040	3065	538	523	12	10	3
7	301,403	4717	774	173	163	8	5	1
8	289,723	4002	463	136	126	8	4	1
9	224,267	2473	231	75	67	8	5	2
10	258,278	3442	550	122	113	11	7	2
11	242,660	2826	416	94	83	6	4	1
12	230,769	2935	381	104	90	7	5	2
13	175,580	1922	183	63	55	9	7	3
14	161,185	1768	163	65	55	7	7	4
15	151,799	1823	212	45	41	5	3	1
16	182,431	3049	436	92	85	6	3	3
17	137,595	2229	489	90	80	6	4	2
18	142,572	1908	315	78	66	6	5	3
19	141,666	2361	343	87	83	3	3	1
20	104,470	1072	95	40	37	5	4	1
21	74,494	1212	175	38	36	5	5	1
22	63,641	494	60	18	18	2	0	0
Total	5,073,357	78,065	11,341	2551	2328	178	128	50

^a: refers effective number of alleles.