##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 1888356841 HG02015_chrY 38619282 + 10496 38613939 HG002_chrY 62432599 + 4406 62432577 1
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1674	1	0
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719	0	1
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7	120	95
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97	0	5
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779	0	5
873	0	5
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564	5	0
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578	5	0
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535	5	0
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374	5	0
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50680	1	0
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8	7359	0
121	8065	17719
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86	0	5
280	182711	135047
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7961	0	1373
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3417	36648	8892
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8	11447	3245
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71	5	0
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32	12	0
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4033	0	8
3940	4	0
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3715	1	0
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929	12	0
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63	4	0
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3728	1	0
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534	0	2
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4072	3374	3374
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20986	101864	25203
23351	51455	29504
330	1	0
244	0	1
130	0	1
164	0	2
83	4	0
3	0	3
158	2	0
267	1	0
6271	0	1747
418	1	0
195	498	0
238	0	125
43	0	125
61	0	3359
70	0	250
145	4237	0
95	6230	0
3529	0	125
503	2	1124
16	0	125
8058	1	1
3001	125	0
3030	0	625
47	0	999
16	0	125
123	0	125
78	0	125
145	875	0
26	1124	0
9237	250	0
909	0	500
3303	587	1212
52	3999	0
37	250	0
13536	1918	2918
42	1000	0
2047	1	0
7403	3376	0
3469	2	1876
390	0	125
570	1	0
62	125	0
411	0	1
254	0	125
560	0	1
332	0	7
3	7	0
240	124	0
1300	1	0
1500	0	1
13297	125	0
34022	4	0
7813	0	1
53099	0	4
23554	1	0
8868	3	0
27612	0	2
42094	0	2
51805	1	0
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35359	4	0
13515	1	0
51921	0	3
16844	2	0
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21365	0	1
5936	0	1
56926	0	16
17835	1	0
1595	2	0
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13926	0	3
29309	4	0
9241	1	0
52516	0	1
713	0	1
304	0	4
36	4	0
4645	0	5
20637	1	0
1994	2	0
5505	0	1
8384	6	0
4640	4	0
35	4	0
12052	0	8
17061	0	26
4801	0	1
37001	4	0
7825	0	1
9736	4	0
57	4	0
4813	8	0
34602	0	1
29939	1	0
4233	1	0
6696	0	1
23839	0	1
5698	1	0
131852	0	1
112956	47076	0
24189	1	0
20065	0	1
3632	6	0
9799	6	0
5613	12	0
102	1	0
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14253	1	0
17033	0	3
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28410	0	1
655	1	0
22669	0	2
4	4	2
687	1	0
22	0	1
7034	10	0
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11	84	1
17	12	0
22	1	0
1	11	0
11	2	0
27	1	0
64	12	0
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38269	8	11
30535	0	1
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26732	6	0
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13434	0	1
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8871	1	0
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6076	0	2
11466	0	1
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483	10	0
3	0	7
11662	1	0
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622	0	1
2687	0	1
4076	8	0
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9157	2	0
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27522	16	7
897	0	1
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2157	0	1
2803	2	0
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29	0	2
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4636	0	1
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1583	4	0
3838	0	4
1296	4	0
27830	26	0
34	26	0
287	0	15
181	2	0
12	0	2
28	0	2
22353	0	12
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9840	2	0
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5451	0	2
12474	0	4
24097	0	2
9551	1	0
2265	1	0
20069	1	0
909	10	19
2130	0	3
218	0	9
15752	0	1
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14529	2	0
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11314	0	1
40950	1	0
1105	4	0
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2688	1	0
625	3	0
105	0	1
8071	0	9
22	0	1
4059	0	4
15353	0	1
12728	0	1
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21	31614	0
6326	5	0
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611	1	0
38575	0	1
4298	0	4
1723	0	1
3988	4	0
54	0	1
4867	0	4
19563	0	1
21029	40728	20758
38	1	0
14	1	0
20988	0	1
8970	0	1
58364	0	6
31354	100030	99121
4868	4	0
66	2	12
34	4	0
46	0	4
39	0	8
57	4	0
35	8	0
3330	0	4
3388	0	5
3851	0	1
20981	1	0
4091	0	1
10	0	1
677	77941	50911
6035	9570	57
435	1	0
158	0	4757
15121	1	0
4459	0	10850
36832	40207	6149
31814	1	0
5357	8	0
1219	1	0
2012	0	1
3204	0	1
12158	0	2
4110	0	12
1677	0	2
9596	0	8
33129	0	3
3363	0	4
1629	0	1
218	1	0
252	1	0
146	0	1
322	0	1
412	1	0
94	10961	1365
33319	0	1
5434	1	0
18752	11495	0
30550	18	0
46449	0	6
6970	1	0
12562	1	0
6289	1	0
64	1	0
17	1	0
1603	1	0
137	1	0
3962	33074	15807
5866	0	1
5106	1	0
6792	1	0
2173	0	2
7681	0	1
814	4	0
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3060	1	0
4982	1	0
6250	4	0
1620	0	4
14831	2	0
688	24506	0
24	4	0
13643	0	6
4905	10	0
1436	0	2
4301	0	10
23113	0	1
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7215	2	0
478	1	0
17	19093	0
4	2	0
20356	0	1
1423	4	0
224	0	4
7159	0	1
7662	0	6
2858	0	6
4341	1	0
1065	0	4
17664	1	0
7347	1	0
1693	1	0
39998	0	1
1509	76031	54616
6804	0	2
14	0	2
40312	2	0
18	0	1
6785	1	0
2103	0	1
1291	124217	85912
13489	20416	0
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2767	2	0
15515	0	12
67	4	0
17292	1	0
10415	1	0
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21450	0	1
195	0	8
18677	4	0
3988	1	0
10190	0	1
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913	0	1
21666	1	0
4139	0	1
3377	2	0
483	2	0
15	4	0
4	6	0
28	0	1
4342	0	2
979	27234	1
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262	0	6
16313	1	0
9745	0	4
26	0	4
22528	0	8
31793	0	1
9942	0	3
3983	4	0
25	4	0
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1442	0	1
8680	0	1
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900	1	0
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8816	0	4
2380	0	1
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4111	0	3
70	0	520
1114	2	0
1721	1	0
291	0	1
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4101	2	0
28030	1	0
25541	4	0
4671	0	2
18594	1	0
2227	0	3
15707	1	0
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1886	1	0
14064	6	0
35694	1	0
16550	1	0
16370	0	1
2991	11136768	35834650
1988	20	0
3533	5	0
3598	0	290
6788	0	5
3566	10	0
8	5	0
1809	5235	1712
63	40	0
5	5	0
3	25	0
6363	25	0
13729	19825	2913
1051	0	1
6	6900	11737
1962	7267	21766
5	0	2
2733	0	7257
3475	0	5
2177	36989	38068
1418	0	5
4342	5	0
396	0	7072
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1013	0	1
289	0	4494
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169	0	3548
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532	10	0
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30717	0	5
3564	3539	0
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4909	5	0
1758	42584	7048
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1737	0	15
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1446	3542	3557
359	0	5
1725	3554	0
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38	10	0
5282	0	3554
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1705	13704	13715
13655	944	4478
22	0	10
15990	10	0
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5437	3535	0
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3370	15	0
89	0	1
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2810	0	15
545	15	0
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164	25	0
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1233	1	0
494	0	20
120	5152	1592
80	0	15
1233	1	0
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1778	0	15
1808	40	0
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830	3520	0
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11732	0	1
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61	40	0
31102	0	3514
45	0	155
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10103	3503	0
5828	0	15
24	15	0
40	0	10
321	5	0
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1438	30	0
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389	1	0
1297	0	1
245	4	0
1566	5	0
389	1	0
1527	5	0
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1020	1	0
447	2636	13156
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26989	0	1268
4452	5	0
37648	0	2
32730	0	4
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2412	0	1
350	0	6
3165	1	0
7821	0	3
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12768	3	0
21	0	36
744	0	1
2117	4	0
2677	2	0
4328	12	0
928	1	0
6743	0	4
1329	0	1
1220	1	0
6251	0	3
6451	0	1
5770	19	0
1776	0	3
2033	0	1
3697	2	0
866	1	0
6134	0	1
109	0	1
2373	1	0
1036	1	0
43	0	1
1026	2	0
1707	1	0
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2723	3	0
45	0	6
11	0	3
2374	1	0
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3104	0	33
22742	0	1
28566	0	1
2776	0	1
49539	2	0
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2146	1	0
3356	1	0
17	6	0
2040	0	1
6977	0	4
68	0	4
6	2	0
37	0	4
134	4	0
716	3	0
4172	0	1
1543	4	0
475	0	1
3616	6	0
125	38	0
1489	1251	0
1129	0	3
4424	0	6
120	1	0
466	0	3
159	47	0
31	74	0
27	0	58
657	38	2
66	0	7
9	0	17
36	0	34
2	0	8
30	7	0
7	0	6
1	8	0
27	30	0
1	0	1
30	0	7
12	0	9
29	16	116
10	0	1
10	4	0
12	0	2
36	0	1
22	1	0
38	0	5
6	0	1
5	0	1
12	13	1
30	0	6
6	5	0
6	57	2
6	0	1
21	80	40
12	7	0
7	17	0
6	0	6
4	0	1
18	1	0
2	5	0
18	50	29
45	0	1
2	6	0
17	0	1
25	4	0
7	0	2
6	22	9
52	156	8
22	57	9
21	5	0
33	1	0
41	0	1
49	3	0
15	3	0
44	0	1
2	0	5
12	3	0
27	3	0
57	3	0
21	3	0
59	17	0
2	0	2
9	3	0
9	25	1
27	0	3
33	1	43
78	5	0
95	0	1
50	101	15
11	0	2
79	2	0
29	4	0
36	0	6
32	4	0
66	4	0
70	4	0
60	0	1
6	1668	1
56	0	5
53

chain 354677997 HG02015_chrY 38619282 + 6268821 10069025 HG002_chrY 62432599 - 52562439 56521946 2
17919	0	4
43	1	0
16942	0	6
8932	0	5
2378	1	0
5861	8	0
10314	4	0
4157	2	0
1	11	0
5801	0	2
2480	0	3
697	0	2
7192	4	0
20263	0	10
73	0	1
26	4	0
3723	0	1
5068	0	1
1103	0	121774
35	0	6
5692	18	0
402	0	1
4199	0	16
51	0	1
49	2	0
3693	0	2
358	0	1
5812	2	0
31	0	8
786	3	0
1505	0	1
989	0	1
2439	18	0
4586	2	0
99	0	8
1691	0	5
2002	0	1
356	0	13
471	0	1
3398	1	0
1930	35	1
12	8080	12950
102	0	1
400	0	1
278	0	1
92	0	1
283	0	1
184	0	1
170	0	2
8	0	12
123	0	1
341	0	1
162	1	0
480	1	0
60	0	1
9	0	1
13	1	0
12	0	1
4590	8	0
7	14	0
814	3	0
1508	0	1
821	2	0
32	0	2
2942	1	0
4187	4	0
99	0	4
3716	2	0
356	1	0
8	13	0
5802	2	0
823	3	0
1508	0	1
821	6	0
28	0	4
2948	1	0
4168	0	2
114	4	0
412	0	1
3302	1	0
356	2	0
3892	1	0
1930	29	3
3122	4	0
29	0	2
2546	0	18
4570	2	0
110	8	0
1699	0	5
2015	1	0
356	1	0
8	12	0
465	1	0
15607	6	0
108	0	4
412	1	0
3302	1	0
356	1	0
8	12	0
11531	0	18
4580	0	6
101	4	0
1693	0	5
11315	2	0
7127	0	2
112	0	4
4545	0	1
5333	34	4
793	3	0
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2546	0	18
402	0	1
1228	0	20314
3090	0	4
7938	1	0
1937	22	0
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106	0	2
422	0	1
12620	0	8
7271	0	2
1693	0	5
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2294	1	0
830	0	2
40	2	0
2556	0	18
4582	8	0
96	4	0
393	1	0
3303	1	0
356	2	0
1	11	0
470	1	0
5339	22	0
6098	1	0
4209	0	6
2580	0	3
1570	1	0
2444	1	0
1440	1	0
823	0	1
1102	0	2
9	30	0
3164	0	2
117	1	0
2952	0	20277
4030	0	6
108	0	2
2	6	0
422	0	1
1301	5	0
2003	1	0
358	1	0
269	3	0
210	1	0
2117	1	0
1630	0	2
1716	1	0
3002	2	0
7127	6	0
534	1	0
3303	1	0
356	12	0
471	1	0
3402	0	1
1940	0	28
783	0	3
1505	1	0
842	0	4
26	2	0
7156	4	0
100	6	0
1692	5	0
8166	24	0
5723	18	0
4584	0	6
3794	0	1
356	0	13
471	0	1
3402	1	0
823	0	1
1102	0	2
9	30	0
3134	4	0
26	0	2
117	1	0
2965	4	0
4013	2	0
110	2	0
426	0	1
191	3	0
1109	5	0
4637	0	1
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12245	2	0
98	2	0
4325	3	0
210	1	0
2117	1	0
3348	1	0
3006	10	0
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32	2	0
106	0	2
1694	5	0
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3143	2	0
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1978	12	0
94	0	2
8750	1	0
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5723	18	0
4582	0	8
96	0	2
13008	6	0
3113	4	0
2072	2	0
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20154	4	0
109	2	0
3715	0	1
623	0	20265
4	0	3
5675	1	0
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1701	5	0
2015	1	0
355	1	0
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465	1	0
5337	32	0
3125	2	0
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3716	0	1
355	0	1
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465	0	1
5337	4	0
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14	16	0
2570	0	18
396	1	0
4174	0	2
37	0	4
52	1	0
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4064	14	0
471	1	0
5343	0	32
783	0	3
1505	1	0
838	0	6
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4544	0	6
116	4	0
13087	0	2
5186	2	0
1981	0	2
114	0	6
9867	18	0
10	4	0
20715	0	2
89737	0	1
29676	6	17
27	0	6
10417	0	20
38150	0	1
49322	1	0
5	0	1
11	3	0
45	21	0
6	0	12
195	8	1
2634	1	0
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13103	8	0
30	2	0
2259	0	1
68349	1	0
3763	17	0
25288	0	3
24841	1	0
35869	0	1
6452	1	0
10138	44	0
15790	0	2
1696	4	0
16471	0	2
13047	3	0
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18560	0	2
3669	0	6
177	0	1
9938	4	0
3002	0	1
12602	1	0
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10425	2	0
13617	2	0
4782	0	2
48101	0	2
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2488	18	0
8493	2	0
11240	1	0
665	0	52
117	26	0
95	0	7
10569	9	0
2483	1	0
2130	2	0
48639	1	0
14045	1	0
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407	12	0
45525	6	0
140	6	0
109307	4	0
6052	4	0
86	8	0
36801	0	1
21023	1	0
3955	0	1
2089	1	0
10656	4	0
17169	0	5
1233	20	0
41	0	12
24372	0	2
6137	46	0
2	2	0
8	22	0
6271	0	1
2652	0	1
43025	0	1
7511	0	1
14761	0	1
80751	2	0
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51966	2	0
5936	2	0
14	0	8
35746	16	0
99	0	4
28953	0	1
13724	1	0
58953	0	8
10989	0	1
1694	0	8
48	0	4
53244	0	24
17494	2	0
3382	5	0
25471	2	0
4232	0	1
46331	1	0
3069	2	0
31410	0	1
1931	1	0
2102	32	0
23911	0	8
22273	0	1
830	0	1
2222	0	1
8650	2	0
3674	0	1
9491	50	0
750	0	75
22664	0	1
14253	16	0
8186	0	4
10598	0	4
22731	5	0
19160	1	0
3346	2	0
20	3	7
18	2	0
48216	12	0
82	0	8
130	0	4
765	1	0
3092	2	0
26526	2	0
5764	0	1
4912	1	0
34440	1	0
10062	0	2
14937	2	0
11485	1	0
13430	0	1
19281	6	0
29	0	2
5089	1	0
24222	2	0
8655	4	0
2105	0	1
19501	0	4
2	2	0
26	2	0
3939	0	2
4141	0	1
8108	1	0
9431	0	1
4497	0	12
250	0	1
1372	0	1
21869	0	8
45055	6	0
24713	0	2
55504	0	1
38219	1	0
28597	8	0
2673	0	1
1884	4	0
48578	1	0
31633	1	0
2935	0	4
36042	0	1
2839	0	1
104177	0	1
57239	15778	0
969	0	28
99015	1	0
27045	0	8
11393	0	2
8083	4	0
51320	3	0
11829	0	2
4	0	2
1725	10	0
35214	0	2
66631	1	0
10503	2	0
3642	0	10004
4052	8	0
4	4	0
59	12	0
12214	0	9
2308	0	3
5864	0	27
113	0	2
28	0	3
27	0	3
252	29	0
41	29	0
55	0	2
4713	0	1
11167	0	1
5950	6	0
5732	6	0
17684	1602	0
322	0	1
2755	2	0
1755	0	1
3328	20	0
59	2	0
43	0	2
26	0	6
2	4	0
172	8	0
176	0	1
364	0	1
1701	0	1
999	0	2
687	4	0
1023	0	14
1979	0	2
2334	0	1
1400	0	4
32	1	3
886	0	2
320	0	1
375	2	0
2675	20324	0
8061	0	1
285	20	0
569	1	0
1721	0	4
311	0	1
311	1	0
292

chain 10008407 HG02015_chrY_random0000683 185577 + 10570 116859 HG002_chrY 62432599 + 53284444 53390704 3
8527	0	5
10605	10	0
14143	0	5
25700	5	0
5315	0	1
13999	0	15
196	15	0
7916	5	0
1244	20	0
3638	0	15
1720	0	5
469	20	0
12742

chain 10005788 HG02015_chrY_random0000684 180727 + 10570 116849 HG002_chrY 62432599 + 53284444 53390704 4
8527	0	5
10605	10	0
14143	0	5
10629	5	0
15071	5	0
5315	0	1
13999	0	15
196	15	0
7916	5	0
1244	20	0
3638	0	15
1720	0	5
469	20	0
9604	0	15
3123

chain 372803 HG02015_chrY 38619282 + 25527014 25530959 HG002_chrY 62432599 - 37698898 37702843 5
3945

chain 1006 HG02015_chrY 38619282 + 1890352 1890364 HG002_chrY 62432599 + 1884992 1885004 6
12