##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 2118456388 NA18612_chrY 72760757 + 0 31407351 HG002_chrY 62432599 + 8 29370600 1
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10	29	0
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121	27	0
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41	8	0
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2164	0	370
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890	0	4
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73	0	4
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51	0	2
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102	4	0
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39	0	4
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584	1	0
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1642	21	11
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1	169	0
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916	0	8
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681	15	0
31524	1	0
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8546	1	0
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6066	0	7
4002	0	1
5798	1	0
4439	1	0
36628	0	4
8268	0	4
1301	8	0
49	12	0
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38422	1	0
37915	0	1
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18	2	0
7631	0	3
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625	0	8
34478	1	0
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46464	0	16
47	0	8
11775	0	2
4376	0	3
27180	8	0
23416	0	12
318	10	0
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6585	0	2
486	12	0
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3280	4	0
79	8	0
5979	0	4
2054	0	2
15733	4	0
6	0	7
2772	1	0
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155	29	0
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1267	0	4
1	0	1
4	0	5
5	0	20
5502	0	2
351	2	0
3668	0	1
296	0	6
1381	8	0
49	4	0
11530	3411	3411
1135	0	1
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286	0	1
1908	1	0
1762	2	0
355	0	2
6817	0	1
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57430	4	0
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7978	2	0
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1481	5	0
3293	0	1
8582	0	1
30977	0	1
3247	0	9
4305	15	0
677	3	0
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9545	1	0
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3035	0	1
3930	2	0
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1891	0	1
17378	2	0
2	19	0
21	25	0
153	0	69
1225	0	1
55820	1	0
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34	0	16
7034	0	2
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14997	1	0
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640	1	0
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163	4	0
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944	3	0
15	1	0
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373	0	12
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15775	13	0
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23	0	4
2757	1	0
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161	1	0
47	2	0
19	0	4
3710	0	2
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21434	1	0
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7477	1	0
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2000	3	0
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23	0	4
1736	4	0
3620	0	8
4228	0	1
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5597	0	4
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2780	8	0
118	0	8
74	28	0
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2518	0	6
784	8	0
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17974	4	0
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8	0	3
227	4	0
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348	0	4
5710	5	0
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399	0	4
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4295	1	0
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1540	0	1
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608	4	0
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84	2	0
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8545	1	0
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7837	1	0
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1114	1	0
3949	8	0
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1187	2	0
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328	12	0
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3	0	8
21809	0	6
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15	0	1
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38748	3	0
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14	0	1
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3	0	14
1293	4	0
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3712	2	0
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16	4	0
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67	4	0
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2287	0	1
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1081	1	0
1992	1	0
3211	0	26
7069	12	0
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2	2	0
7763	1	0
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95	0	4
3582	1	0
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7962	1	0
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763	0	1
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3270	1	0
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118	8	0
7094	1	0
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184	8	0
239	0	4
2478	10	0
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5445	0	1
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4160	1	0
6192	1	0
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5292	6	0
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65	8	0
1098	2	0
6613	2	0
533	12	0
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379	2	0
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25	0	2
3569	0	1
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392	0	8
126	0	4
79	8	0
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107	4	0
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1166	0	1
88	2	0
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2399	1	0
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773	1	0
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750	1	0
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42	2	0
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19	0	2
4776	1	0
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461	1	0
3565	2	0
67	0	2
1979	1	0
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38	0	2
9058	1	0
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30	0	4
8718	0	1
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25	20	0
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1999	0	2
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88	4	0
616	0	4
24119	6	0
32	0	2
6	0	2
1675	0	2
4	0	1
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7	0	1
31317	1	0
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426	4	0
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6448	0	1
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1713	1	0
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175	0	12
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24752	4	0
6722	1	0
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38995	1	0
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39	0	16
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32	4	0
2858	0	6
4078	3371	3372
2125	6	0
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3699	1	0
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42	2	0
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1	2	0
1639	1	0
16167	3457	3457
16158	1	0
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59	13	0
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9557	0	1
13	0	1
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33	0	2
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4	12	0
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8	7	0
6718	2	0
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21	0	2
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644	39673	39663
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12251	2852	2852
127	2	0
2	623	0
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367	4	0
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8987	0	25
2245	2	0
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184	0	2
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8	10365	3869
1924	125	0
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145	875	0
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210	3803	5927
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1128	12506	3872
3848	5	0
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7	432	0
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186	0	5
317	0	5
150	0	10
250	5	0
707	15	0
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506	11115	38724
2590	5	0
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320	0	1
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21	5	0
340	3504	0
717	54275	201464
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3479	8961	1901
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365	3526	17721
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370	1	0
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810	17725	0
543	15	0
4412	15	0
60	9505	20157
1146	0	5
1708	79	2508
148	2	0
1985	2411	2411
174	1189	8387
3101	9675	2412
781	0	3
5436	0	2416
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152	3	0
38	0	2
1408	2	0
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1015	5	0
60	0	10
215	15	0
28	5	3569
3735	1	0
4942	5823	0
278

chain 314890584 NA18612_chrY 72760757 + 23729341 27144369 HG002_chrY 62432599 - 35816423 39235984 2
2090	4	0
15353	1	0
21852	1	0
12725	0	1
39658	0	2
20310	0	8
4261	1	0
16861	1	0
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10125	1	0
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2452	3	0
14909	0	1
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271	0	2
34	4	0
5213	1	0
2634	2	0
373	3945	3945
385	0	2
904	0	1
1745	2	0
5221	2	0
286	0	1
1642	0	2
12206	0	2
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15899	1	0
1182	0	1
4563	2	0
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2714	0	6
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2442	1	0
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416	0	1
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14	0	1
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814	0	1
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99	2138	2138
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19	2	0
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3988	3	0
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195	0	1
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667	1	0
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38	0	8
15548	2	0
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44	0	2
24456	6	0
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1551	0	20
7323	0	11921
71	0	2385
1774	0	1
5245	10593	3437
2382	0	1
22402	1	0
94	2138	2138
99	0	1
20399	0	2
5927	1	0
6936	0	1
5082	0	4780
2089	1	0
715	0	4757
650	17958	6035
8026	0	1
8608	3	0
3200	0	1
1574	0	1
1301	3	0
9259	0	14
4124	3	0
740	1	0
913	2	0
6200	0	1
3430	0	8
19428	1	0
13695	0	2
3391	0	4
3365	4	0
154	4	0
34	8	0
78	0	8
9966	1	0
24150	0	3
97	0	1
3169	0	1
51451	18	0
5547	1	0
9979	0	8
5	0	1
1390	0	1
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600	0	2
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610	0	2
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625	1	0
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1594	2	0
28426	1	0
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6932	1	0
5079	0	2
6737	2	0
11694	12	0
847	0	1
141	1	0
4057	1	0
6022	1	0
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29	4	0
6985	1	0
5431	0	2
5451	0	3
6615	0	1
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113	0	2
94	2	0
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211	0	3
147	1	0
15	0	3
120	2	0
69	0	5
79	0	1
69	3	0
5	1	0
158	4	0
288	1	0
40	0	1
200	0	152
5	0	2
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61	0	2
131	0	1
72	12	0
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48	1	0
315	14	0
104	0	2
111	1	0
69	7	0
3	5	0
20	9	0
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50	0	2
72	2	0
25	0	7
218	0	1
67	0	28
4	32	0
53	0	2
114	0	3
386

chain 61854737 NA18612_chrY 72760757 + 72084154 72756235 HG002_chrY 62432599 + 61656421 62432584 3
2857	0	1
14479	1	0
24879	0	31794
705	0	1
386	0	15
5769	0	1
2804	897	4432
3367	1	0
3534	0	1
7068	0	1
2705	0	14139
5649	15	0
2235	1	0
1284	0	15
17560	25	0
3551	0	25
7054	25	0
1881	1	0
1645	25	0
6930	0	15
150	0	25
215	0	21200
1431	40	0
3493	40	0
1686	0	15
1233	1	0
494	0	20
74	0	25
14	4069	28603
2343	0	1
494	20	0
66	40	0
6429	1	0
494	0	20
66	0	40
5985	0	3502
161	0	1
1489	0	5
5088	10	0
846	0	3514
4033	0	1
15820	0	15
24	15	0
371	5	0
3493	5	0
909	0	3498
552	30	0
5528	5	0
3475	5	0
32	0	3508
7901	3510	0
1044	1	0
1997	1	0
456	0	20
2570	5	0
20210	0	2
9848	0	2
791	0	2
1854	5	0
35202	2	0
2446	0	2
32615	4	0
16	17	0
99	0	4
3329	0	1
5649	0	2
5904	0	4
2763	0	9
1716	0	1
1445	1	0
6795	1	0
12118	0	1
5290	3	21
34739	0	1
214	15	0
3008	2	0
12789	0	36
5539	2	0
4328	4	0
28701	19	0
1776	0	3
1309	1	0
724	0	1
1972	4	0
1725	5	0
866	1	0
16126	0	1
2723	1	0
45	0	6
7336	0	1
8120	0	5
407	1	0
1864	6	0
7215	0	1
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915	0	3
3142	14	0
8900	1	0
658	0	16
90	80	0
2998	0	33
11481	1	0
4807	0	3
6451	0	1
343	0	2
4828	0	1
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530	2	0
2613	1	0
1095	0	4
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6099	0	1
73	12	0
272	0	2
2724	2	0
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5214	2	0
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8018	29	0
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106	6	0
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14	4	0
20	8	0
28	0	54
3	1	0
6	0	5
6	0	1
5	0	1
12	13	1
29	7	7
13	197	60
21	34	11
12	0	2
20	12	0
16	4	0
1	10	0
15	19	14
12	1	0
13	0	17
3	0	1
14	8	0
12	7	0
3	0	1
2	1	0
13	4	0
5	20	31
43	128	0
3	0	2
22	53	9
21	5	12
11	0	12
6	6	0
24	0	1
11	5	0
28	8	23
11	3	0
1	0	4
54	7	0
5	3	0
4	0	5
18	3	0
21	1	0
17	4	19
21	3	0
51	0	3
27	22	1
27	0	3
14	0	4
8	1	0
35	3	0
15	5	9
8	0	61
51	0	1
43	0	1
17	1	0
33	63	195
15	4	0
52	2	0
84	4	0
5	0	5
7	0	5
38	0	1
6	1420	1
56	0	5
55	4	0
5

chain 3740832 NA18612_chrY 72760757 + 20076223 20115889 HG002_chrY 62432599 - 42850342 42889998 4
8542	0	1
11422	4	0
6526	8	0
4702	1	0
5797	2	0
881	0	4
1781

chain 3058736 NA18612_chrY 72760757 + 22425540 22457835 HG002_chrY 62432599 - 40507615 40539913 5
6287	0	1
5505	0	2
20503

chain 372672 NA18612_chrY 72760757 + 23991869 23995814 HG002_chrY 62432599 + 26349701 26353646 6
3945

chain 327177 NA18612_chrY 72760757 + 19387116 19390572 HG002_chrY 62432599 - 43575591 43579047 7
3456

chain 322611 NA18612_chrY 72760757 + 15454871 15458279 HG002_chrY 62432599 - 47507067 47510475 8
3408

chain 201400 NA18612_chrY 72760757 + 24711568 24713690 HG002_chrY 62432599 + 25646281 25648403 9
2122

chain 201400 NA18612_chrY 72760757 + 26313994 26316116 HG002_chrY 62432599 + 24031131 24033253 10
2122

chain 1055 NA18612_chrY 72760757 + 12306477 12306488 HG002_chrY 62432599 + 11945862 11945873 11
11