##matrix=axtChain 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91
##gapPenalties=axtChain O=400 E=30
chain 2170757327 NA19443_chrY 56618180 + 34 24722215 HG002_chrY 62432599 + 140 24162561 1
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1121	5	0
801	6	0
535	2	0
753	0	2
2892	0	2
938	4	0
1876	8	0
46	5	0
174	0	1
539	2	0
2639	1	0
9175	12	0
1558	6	0
58	174	0
41	6	0
17	18	0
29	6	0
17	18	0
23	23	11
29	0	6
769	0	3
914	0	1
1934	0	1
1395	0	7
176	0	1
1596	128	0
139	0	64
300	0	1
1176	4	0
2	4	0
20	0	10
107	0	2
55	50	0
29	1	56
86	21	0
4	8	0
79	29	0
58	0	8
8	4	0
106	111	3
391	2	0
178	2	0
20	4	0
669	0	1
341	0	4
1292	1	0
1378	0	1
14	0	5
1040	0	95
882	1	0
284	9	0
863	0	1
694	0	3
2055	1	0
4	4	0
1814	170	0
610	0	1
3305	3	0
490	0	1
76	0	4
4248	0	1
41	0	4
22	0	11
9	0	5
6	0	4
121	0	2
50	0	4
947	12	0
146	2	0
40	2	0
1029	6	0
1735	1	0
1797	4	0
1294	0	15
442	1	0
57	0	2
876	3	5
54	0	8
17	0	27
7	40	0
2088	1	0
4423	1	0
2532	0	1
68	1	0
7401	1	0
550	1	0
7071	1	0
965	0	22
1698	308	0
138	4	0
501	0	2
1120	1	0
966	1	0
468	5	0
4499	0	4
677	8	0
21	0	8
73	0	4
230	0	54
25	0	4
5	0	4
79	0	8
794	0	3
2851	1	0
814	3	0
443	6	0
728	0	6
184	0	21
43	12	0
31	0	1
658	0	1
354	0	3
336	1	0
2017	26	0
1561	0	8
5812	62	0
11	4	0
3	4	0
2	2	0
39	24	0
13	1	0
3	1	0
391	1	0
305	0	1
588	0	1
1066	0	1
2424	0	4
2366	14269	1219
1007	1	0
1093	0	4
1749	4	0
793	0	4
283	8	0
455	4	0
389	0	4
1941	0	4
1483	0	14
147	0	1
1252	0	1
1719	27	0
149	0	2
83	0	29
8	2	58
27	0	4
29	1	7
27	6	0
27	0	2
27	0	27
1	0	2
10	29	0
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121	27	0
52	0	2
211	0	4
1400	2	0
14	3	0
1519	3	0
474	3	0
11	1	0
52	8	0
6	6	0
19	23	0
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11	4	0
8	3	0
5	4	0
18	0	1
1167	0	2
4	0	4
858	1	0
306	0	124
1500	4	0
1739	3	0
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11	1	0
81	0	816
11	0	4
199	4	0
45	2	0
1028	12	0
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20	0	4
28	0	4
23	0	4
54	0	16
36	8	0
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46	16	0
96	4	0
4	0	8
220	0	4
5	0	4
40	4	0
77	4	0
15	0	133
104	0	4
28	0	4
177	0	4
1436	0	142
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211	284	0
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434	0	9
3	0	706
262	0	1
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37	12	0
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3057	12	0
1379	0	12
103	12	0
223	0	64
172	0	4
144	0	20
2091	1	0
1881	1	0
1207	3	0
38	0	309
898	0	1
1503	28	0
512	1	0
141	0	1
1369	0	1
1094	2	0
141	0	3
509	0	4
1643	7	0
876	4	0
974	48	0
63	1	0
57	0	192
31	0	96
108	1	0
18	0	48
48	0	49
218	0	48
1831	1	0
304	1	0
1948	2	0
3640	8	0
1692	0	52
91	104	0
73	52	0
965	0	2
2778	0	4
10	0	9
719	0	1
1618	1	0
2981	0	2
74	14	0
28	63	81
93	0	2
405	0	6
125	6	0
76	0	2
22	2	0
69	0	6
119	0	2
1202	0	4
171	1	0
1319	0	5
827	0	5
302	1	0
7	8	0
269	0	12
57	4	0
436	4	0
80	20	0
103	0	4
32	4	0
41	4	0
119	2	0
374	4	0
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48	0	4
120	0	4
3251	0	3
2	0	5
27	0	3
64	1	0
599	0	1
1	0	2
3105	0	4
57	4	0
11	1	0
12	2	0
488	3	0
738	0	4
403	0	2
935	3	0
894	0	1
2594	0	1
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41	2	0
1035	4	0
2859	1	0
1343	0	2
85	0	7
22	4	0
253	19	0
473	0	1
1463	5	0
1044	1	0
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13	4	0
60	3	0
8	2	0
7	0	1
3	0	12
9	0	3
4	0	1
14	0	2
19	0	7
346	0	1
2088	0	269
516	0	3
19	1	0
168	0	2
269	0	1
442	2	0
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1240	1	0
74	0	1
817	4	0
3741	4	0
12	4	0
43	0	8
4	4	0
29	4	0
112	4	0
71	4	0
302	4	0
14	4	0
68	0	4
32	0	16
32	0	4
19	0	4
37	0	4
524	0	5
621	29	0
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305	1	0
2670	0	4
34	0	8
76	1	0
554	12	0
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45	4	0
30	2	0
81	14	0
2	16	0
690	789	0
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60	0	1
239	0	1
153	1	0
362	2	0
5248	0	4
316	0	1
898	0	4
5122	0	2
2584	1	0
159	1	0
289	6	0
31	4	0
1944	0	1
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195	1	0
2561	0	4
3	0	4
26	4	0
49	211	0
206	1	0
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33	1	0
6	24	0
993	0	2
1183	0	2
365	10	0
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2505	4	0
487	3	0
1863	0	10
37	0	10
1720	0	1
1039	0	1
341	135	0
205	2	0
4575	0	590
295	0	590
2973	1	0
3439	0	4
366	2	0
780	135	0
188	0	3
930	2	0
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1098	1	0
2432	0	1
268	0	1
417	0	1
298	0	1
2414	0	200
418	0	80
19	0	160
22	0	40
3622	3	0
68	0	107
37	10	10
58	0	55
107	0	162
22	0	324
526	8	0
657	269	0
657	1	0
738	0	1
8	2	0
560	0	4
21	5	29
24	9	0
9	5	0
797	2	0
284	0	2
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1281	0	3
166	1	0
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2	0	4
292	0	4
201	0	1
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538	0	1
4168	106	0
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635	4	0
57	4	0
53	0	4
38	4	0
1899	0	4
96	12	0
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10	0	36
99	0	2
284	1	0
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35	1	0
146	0	252
69	396	35
717	0	72
108	0	1
4	0	1
69	1	0
932	0	2
146	4	0
3178	1	0
2534	2	0
442	0	2
548	235	0
1924	318	0
3344	2	0
22	0	12
296	0	2
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321	0	4
114	2	0
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26	2	0
94	4	0
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133	0	118
2	0	2
5	0	12
147	12	0
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1215	49	0
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3	9	0
23	4	0
363	0	3
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315	1	0
61	0	4
72	8	0
431	0	6
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17	5	0
32	1	0
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108	0	15
67	10	0
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49	46	6
34	685	0
63	2	0
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59	50	0
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8	2	0
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39	1	0
1	4	0
85	10	0
530	0	5
559	0	2
235	0	276
58	3	0
2010	5	0
1586	0	8
2496	2977	2955
11	0	4
264	4	0
794	0	3
1734	0	1
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536	0	1
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98	1	0
6	5	0
5	0	3
26	0	61
7	0	24
7	0	3
11	0	8
8	148	10
13	54	0
14	1	3
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3	0	1
6	7	0
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4	26	0
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9	0	1
5	51	0
9	266	0
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34	0	1
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32	13	0
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6	2	0
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10	0	1
8	84	10
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31	43	5
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12	241	19
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48	0	1
90	0	1
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4	0	1
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4	0	7
47	0	2
80	0	23
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1	0	1
9	0	1
3	337	0
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24	0	2
52	0	5
8	0	1
6	0	2
4	0	1
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26	0	10
3	176	0
76	65	20
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9	0	1
9	1	0
7	25	17
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17	4	0
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9	0	1
13	567	70
54	0	1
388	2	0
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244	6	0
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1336	15	0
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967	30	0
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60	2	0
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17	0	20
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481	0	4
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1023	2	0
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439	0	1
908	1	0
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78	64	0
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1057	0	4
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92	12	252
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522	1	0
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207	1	0
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2983	0	1
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1170	83	39
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478	0	4
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647	0	4
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16	148	0
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460	10	0
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705	5	0
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146	5	0
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1445	63	0
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1	10	0
579	1	0
683	183	0
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887	0	2
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70	1	0
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318	0	1
2240	429	87
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2440	1	0
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88	40	0
5	5	0
42	0	1
10	0	13
3	5	0
22	86	19
9	0	15
2	0	1
10	13	2
37	13	0
11	3	0
6	7	0
30	26	0
6	0	12
9	0	10
26	3	0
21	3	0
16	0	4
4	3	0
5	18	0
3	9	0
5	9	0
8	35	0
93	4	0
19	55	0
63	8	3
97	0	16
1047	0	1
74	2	0
5010	3	0
920	0	1
2469	0	4
197	4	0
67	0	4
5470	0	4
319	0	5
582	4	0
4054	1	0
2966	12	0
16	8	0
286	3	0
293	1	0
300	2	0
1169	1	0
435	0	4
161	0	5
3379	4	0
781	0	1
215	2	0
576	1	0
3062	15	3
1179	0	2
9	0	2
971	0	1
784	1	0
11	1	0
188	2	0
447	4	0
40	4	0
907	0	5
161	1	0
3758	1	0
342	0	12
88	0	4
54	4	12
63	4	0
318	8	0
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205	4	0
37	4	0
72	0	4
1916	2	0
571	0	4
219	32	0
5	8	0
1569	1	0
72	0	8
122	2	0
312	1	0
4	11	0
499	0	3
1905	1	0
47	0	1
170	1	0
767	0	69
113	0	5
1370	2	0
8	13	0
1	0	1
52	0	18
917	0	12
6	0	3
760	3	0
38	0	1
300	2	0
872	0	2
1440	1	0
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11	0	2
3763	8	0
197	4	0
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2175	0	4
524	3	0
2061	8	0
1023	13	16
39	0	8
5	4	0
16	16	0
622	1	0
1158	3	0
512	4	0
636	2	0
907	1	0
157	204	184
259	10	0
97	0	1
95	20	0
66	0	10
10	0	5
60	0	5
88	0	1
213	5	0
75	0	5
57	48	0
23	37	0
108	0	1
99	0	1
73	0	15
79	0	20
4141	1	0
2879	0	1
314	113	0
6	47	0
1401	7	0
5455	373	0
36	4	0
1053	0	2
106	1	0
9	1	0
4535	0	34
2080	1	0
1260	4	0
61	22	4
11	4	1
1491	2	0
2924	1	0
1775	1	0
175	0	6
28	0	1
571	1	0
748	1	0
2072	0	1
1489	0	124
451	2	0
4	2	0
437	0	4
5	0	22
403	0	3
279	1	0
1417	0	5
1282	0	10
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2712	0	1
625	1	0
311	1019	0
709	0	1
331	1	0
1927	4	328
46	0	83
53	1	0
30	0	166
25	0	82
7	0	83
2486	0	6
897	0	1
9712	0	11
932	0	1
1054	2	0
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15	0	2
1743	0	1
23	0	1
16	4	0
22	0	4
36	0	2
606	0	2
48	0	2
107	0	2
228	2	0
1227	0	20
707	0	117
140	2	0
1170	1	30
5	5	0
1854	2	0
1121	1	0
16	1	0
2662	0	9
2101	0	1
5744	8	0
412	2	0
635	0	1
806	2	0
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648	1	0
1885	8	0
54	0	1
8	0	7
5	0	1
47	4	12
11	1	26
32	4	0
9	27	195
14	4	0
10	0	8
8	0	2
14	1	0
1	0	4
13	0	5
6	6	0
27	0	1
37	3	0
1	3	0
4	0	2
20	0	17
1	0	2
9	0	2
22	0	2
30	0	6
18	0	9
17	0	8
6	0	20
1	0	7
12	0	34
17	0	2
10	0	2
8	0	1
10	2	0
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10	0	4
8	0	2
6	0	18
4	2	0
6	0	6
4	2	0
8	0	1
9	0	2
14	0	2
6	0	3
8	0	4
8	0	42
4	0	4
26	2	0
6	0	2
14	19	76
16	0	2
28	242	357
46	0	10
6	28	0
18	0	2
3	0	1
34	0	2
54	12	0
1529	0	2
3421	8	0
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1614	0	2
342	11	0
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402	2	0
825	0	6
175	0	5
23	0	180
1299	0	1
1569	0	756
2096	1	0
289	1	0
266	0	43
47	0	86
1152	0	1
6122	0	22
755	0	17
587	3	0
448	0	1
332	6	0
76	1	0
15	3	0
5	0	1
162	0	26
336	0	2
102	0	4
2645	1	0
162	0	2
1202	0	4
1181	0	1
470	0	4
368	0	2
13	0	2
1275	4	0
3336	0	4
424	4	0
79	4	0
188	0	4
981	0	4
1240	0	2
1226	0	1
508	0	8
1517	0	4
1756	8	5
11	0	1
2163	5	0
425	0	2
1144	0	14
114	3	0
59	0	48
31	0	8
1	0	1
17	8	17
22	0	1
5	0	11
2	0	4
11	21	0
61	8	0
9	23	0
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16	0	1
3	1	0
8	1	0
10	6	0
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12	0	1
29	25	0
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4	2	0
11	13	0
3	0	2
3	14	0
86	12	0
53	26	0
169	0	16
1	0	1
83	31	0
231	0	90
6	0	6
1446	2	1
404	0	1
869	0	6
501	14	0
4	2	0
660	0	2
153	639	0
145	0	6
17	1	0
188	0	1
43	4	0
3505	1	0
7816	1	0
1766	0	1
3775	1	0
157	0	1
2568	0	12
2381	0	2
1154	30	0
173	0	90
118	0	30
962	0	1
1452	2	0
536	0	5
1989	0	1
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3842	1	0
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638	0	4
389	1	0
70	0	1
540	4	0
2314	5	0
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774	0	5
171	7	0
2138	1	0
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44	0	1
177	2	0
755	7	0
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168	28	0
11	4	0
302	4	0
17	3	0
1022	8	0
38	0	4
625	14	0
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32	4	0
216	0	2
249	4	0
1230	1	0
485	0	40
15	0	2
183	17	0
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483	4	0
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144	0	2
1015	4	0
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43	4	0
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33	0	12
19	0	4
12	8	0
542	0	1
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584	2	0
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503	2	0
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1744	1	0
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410	39	7
619	0	3
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42	0	3
39	0	6
27	2	0
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16	0	45
287	0	3
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32	0	3
49	0	3
30	7	4
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81	0	3
42	0	6
370	0	3
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39	0	3
42	0	3
84	0	3
93	0	3
25	0	3
36	0	3
68	0	45
71	3	0
39	3	0
19	0	163
241	0	39
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4831	347	0
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300	3	0
3	0	7
4	54	0
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48	4	0
119	344	0
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169	0	2
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306	0	1
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74	0	5
69	0	25
806	0	1
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540	0	296
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1415	4	0
182	0	3
685	0	3
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562	0	13
21	0	1
4739	0	3
1064	1	0
2334	0	8
4197	1	0
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63	0	4
220	2	0
42	0	4
8	0	4
11	0	3
1	11	0
35	11	12
3234	1	0
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872	5	0
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33	0	1
732	8	0
248	0	4
111	0	24
50	0	172
29	0	8
69	0	2
665	4	0
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765	0	84
373	252	0
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880	0	2
1624	2	0
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264	3	0
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70	0	4
1187	0	2
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3419	1	0
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1	8	0
68	0	16
149	2	0
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20	2	0
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97	3	0
276	2	0
68	85	82
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36	1	0
3	2	0
19	2	0
182	0	2
112	0	4
1250	39	11
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24	0	5
743	4	0
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61	33	0
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146	0	56
1447	0	3
47	0	341
1168	4	0
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2059	0	1
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107	26	0
34	7	0
24	2	0
183	4	0
662	33	27
753	35	0
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23	3	0
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293	0	1
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68	3	0
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630	1	0
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244	25	0
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34	4	0
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41	5	234
16	2	0
67	0	2
54	0	18
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4737	1	0
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548	0	22
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90	0	4
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73	0	4
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51	0	121
97	41	0
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71	160	77
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173	41	0
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178	83	0
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605	8	0
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25	1	0
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37	0	1
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60	1	0
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2	151	0
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28	1	0
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7	3	0
16	0	1
4	4	3
15	52	12
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15	1	0
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1	32	0
61	0	1
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2918	1	0
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567	0	22
121	4	0
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3	9	0
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12	3	0
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3	1	0
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8	10	37
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15	0	1
8	4	0
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5	0	3
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16	1	0
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8	7	0
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17	1	0
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12	0	1
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1	0	1
11	0	3
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4	0	16
32	2	1
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19	1	0
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42	4	28
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1	0	4
12	0	7
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9	1	0
3	3	0
20	33	83
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3	4	0
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38	0	6
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16	3	0
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12	4	1
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3	0	1
8	2	0
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52	0	3
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38	3	2
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1	0	3
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2866	0	1
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290	3	0
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536	0	1
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2078	4	0
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319	40	0
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174	1	0
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89	2	358
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57	0	7
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86	249	0
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555	0	3
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1870	2	0
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1089	0	4
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1629	0	2
538	1	0
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124	6	0
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2771	2	0
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83	1	0
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1	0	8
5	0	2
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67	0	1
349	0	1
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107	0	1
5	12	31
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8	0	1
1	14	0
16	12	26
88	17	0
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4540	1	0
578	0	4
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390	1	0
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2685	1	0
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163	1	0
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537	1	0
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487	32	0
3075	1	0
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705	1	0
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2778	0	1
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280	0	2
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4116	0	1
1002	0	12
34	3	0
1118	1	0
52	0	4
31	16	0
285	0	2
170	1	0
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663	0	10
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48	0	5
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18	0	5
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12	1	0
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44	0	5
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8	7359	0
121	19097	12166
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1449	13690	22120
10	5	0
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1833	1	0
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293	185131	164484
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699	0	1377
263	40881	20093
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54	5581	0
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96	1	0
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1473	11095	0
693	36691	8892
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289	10	0
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73	0	5
1593	10	0
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29	19085	0
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69	0	15
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1751	5	0
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11530	3415	3411
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78	16	0
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843	1	0
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7905	1	0
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583	12642	12645
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1539	46216	46210
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2529	0	3
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34	4	0
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3925	325	0
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133	31819	83462
43	0	125
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157	6985	2859
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847	0	1
141	1	0
364	0	2
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70	0	4
2596	1	0
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5090	0	1
322	0	3
4637	1	0
26125	0	4
65988	5	0
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25554	12	0
25	0	4
11215	0	4
13117	0	3
1587	4	0
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6748	0	1
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19	3	55
13	11	0
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13	2	0
13	0	2
13	2	0
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18	0	2
167	0	2
21275	1	0
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21691	1	0
4459	1	0
4612	0	3
322	0	1
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64	4	0
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391	1	0
141	0	1
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2264	1	0
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3302	1	0
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1840	0	2
288	0	3
26959	0	1
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4101	1	0
2688	1	0
625	3	0
105	0	1
11329	0	1
358	0	7
3	10	0
464	0	4
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611	4	0
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4867	0	4
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53	4	0
35	12	0
3330	0	4
3370	0	23
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754	16	0
3438	0	1
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84	11	0
1668	0	1
2516	4	0
913	1	0
740	15	0
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195	1	0
9914	0	2
5225	4	0
3316	1	0
3724	1	0
1558	0	11
1457	1	0
4310	0	1
1301	1	0
950	1	0
7	2384	0
6178	0	1
506	0	4757
715	0	1
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4952	1	0
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452	1	0
4481	0	1
352	0	3
5572	0	5
4887	10847	0
31	0	1
614	0	1
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2429	1	0
2383	15371	3437
5676	1	0
849	2384	0
2244	0	1
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10071	0	1
4314	1	0
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3722	1	0
83	8	0
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860	0	1
840	0	3
5169	0	1
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4842	0	1
3432	0	1
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2020	1	0
3434	0	12
753	0	1
18691	0	1
13431

chain 66114112 NA19443_chrY 56618180 + 55872281 56614174 HG002_chrY 62432599 + 61656421 62432577 2
2304	15	0
204	10	0
880	0	10
12258	0	5
1676	1	0
7396	16238	6604
11807	2	3521
154	0	15
1282	0	10603
8029	0	1
3942	0	17673
6660	0	1
3534	1	0
6240	0	14139
829	0	1
1634	0	5
11	10	0
36774	1	0
9600	185	3705
2350	0	15
150	0	25
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150	0	25
3370	15	0
150	25	0
8742	5	0
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494	0	20
74	0	25
14	5079	1599
1328	1	0
494	0	20
66	0	40
20409	0	1
513	20	0
61	40	0
6642	0	30
225	0	15
64	40	0
61	0	1
323	0	1
739	0	15
784	0	20
300	10	0
156	0	45
122	20	0
103	0	1
38	0	1
598	0	1
186	40	0
247	15	0
525	0	5
348	0	15
577	0	10
517	10	0
156	0	45
122	20	0
103	0	1
263	1	0
373	0	1
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353	15	0
406	5	0
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940	0	10
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384	10	0
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122	18	0
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179	1	0
264	10	0
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320	0	15
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15090	5	0
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14872	3503	0
9731	5	0
909	0	3498
552	30	0
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389	1	0
1297	0	1
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32	0	3508
3459	7012	0
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91	0	1
960	1	0
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1997	1	0
456	0	20
2570	5	0
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491	5	0
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866	1	0
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718	0	30
1588	0	8
11	2	0
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3912	0	12
641	0	6
1	0	2162
1242	30	0
6767	0	5
2128	1	0
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347	0	2
256	2	0
9875	0	1
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782	1	0
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286	0	4
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37	0	4
134	2	0
716	3	0
4172	0	1
162	0	1
1380	1	0
475	0	4
3571	0	6
24	6	0
137	19	0
1489	1251	0
1129	0	3
2403	0	4
2017	0	6
120	1	0
466	0	3
159	47	0
31	29	0
27	58	0
715	42	0
30	6	0
38	0	7
59	4	48
12	8	0
16	25	15
20	24	7
8	1	0
18	0	1
5	0	7
20	0	1
9	0	13
11	1	0
36	0	10
10	0	6
22	2	0
8	0	1
6	0	5
6	0	1
22	4	0
5	0	19
14	2	0
10	0	54
3	1	0
6	0	5
6	0	1
5	0	1
12	90	51
5	1	0
18	143	30
36	0	2
12	0	2
35	34	21
17	19	0
5	1	0
13	0	17
3	0	1
45	4	0
7	0	2
6	23	9
14	3	555
24	3	0
15	5	9
13	78	443
35	4	0
66	410	72
56	0	5
53

chain 14289463 NA19443_chrY_random0000255 223590 + 24 151599 HG002_chrY 62432599 - 45062889 45214480 3
247	1	0
54	1	0
7728	1	0
5776	0	2
8879	0	4
9215	0	1
29074	1	0
6694	0	4
379	0	1
8001	1	0
10645	1	0
4740	1	0
168	2	0
4262	0	2
10524	0	5
13	0	5
972	2	0
6388	1	0
2348	8	0
533	4	0
7621	0	1
81	0	4
69	12	0
50	0	24
7111	1	0
4119	2	0
3085	0	2
1151	1	0
1054	0	1
8116	1	0
897	0	1
1540

chain 6789169 NA19443_chrY_random0000255 223590 + 151599 223588 HG002_chrY 62432599 + 17171910 17243900 4
11602	4	0
239	0	4
2478	8	0
19	2	0
18646	0	4
14757	1	0
9014	0	1
5292	0	2
4117	1	0
5654	0	2
35	0	4
120

chain 4354070 NA19443_chrY 56618180 + 17688319 17734534 HG002_chrY 62432599 - 45214480 45260689 5
13217	0	4
18646	2	0
19	8	0
2478	0	4
239	4	0
11602

chain 1190969 NA19443_chrY 56618180 + 17302167 17314807 HG002_chrY 62432599 - 45634118 45646761 6
1386	0	6
6455	1	0
4090	2	0
706

chain 322143 NA19443_chrY 56618180 + 15438336 15441748 HG002_chrY 62432599 - 47507067 47510475 7
2617	4	0
791