##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 1869463865 NA18952_chrY 54292867 + 26 54281742 HG002_chrY 62432599 + 79 62432577 1
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823	1	0
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92	0	816
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220	0	4
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1043	5	0
13	5	0
212	5	0
27157	1	0
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1434	1	0
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5555	18	0
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4578	0	4
5101	0	4
21582	0	22
10	0	2
13	0	2
1	0	2
12538	0	1
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1328	8	0
32311	4	0
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3165	0	5
12304	3	0
5054	0	5
4668	5	0
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1630	20	0
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17872	0	3361
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311	1	0
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1156	0	5
594	5	0
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572	5	0
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77	5	0
4948	5	0
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572	15	0
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1159	5607	0
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4821	15	0
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50	5602	0
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5596	10	0
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4432	0	5
497	5	0
561	5	0
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630	0	5
4959	10	0
373	0	654
187	10	0
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781	10	0
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15812	1	0
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127	0	10
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413	0	1
237	0	5
485	15	0
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92	0	1
698	5	0
341	0	15
132	0	5
452	0	5
2	0	15
33	0	1
628	5	0
188	20392	30010
351	4	0
2	6	0
9	5	0
21	0	20
11	0	20
45	0	84
72	0	50
11	5	0
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4	2	0
115	70	0
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89	0	3
3	0	2
39	35	0
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66	15	10
20	5	5
99	0	10
69	0	6
23	0	4
3	0	1
16	14	29
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32	0	10
10	5	0
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4	0	8
15	0	5
100	5	0
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30	0	10
8	0	6
17	0	15
4	5	0
36	0	25
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33	16	21
38	1	0
77	5	0
59	5	0
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39	5	0
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9	0	5
11	0	6
2	11	0
81	5	0
53	0	10
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90	20	0
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20	0	5
145	0	1
65	0	5
26	0	40
13	0	45
66	0	25
129	5	0
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32	30	0
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6	1	0
163	0	25
3	45	0
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31	1	0
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96	4	0
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46	35	0
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107	8	9
24	75	0
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18	90	15
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6	79	0
141	5	0
259	10	0
633	0	5
356	176774	110824
2167	0	5
1373	0	5
569	0	1
2171	1367	0
354	1369	0
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203	137159	39614
8744	0	5
234	0	10
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57	0	5
426	0	5287
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1367	0	10
1944	23789	10076
368	0	5
1345	5	0
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898	1	0
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1746	32771	16546
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202	0	5
7183	0	5
1458	15	0
2068	18727	18707
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1274	0	5
1880	10	0
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3624	0	5
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45	0	5
96	1	0
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1473	11065	0
693	36579	8892
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289	10	0
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566	30	0
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7	0	325
4	0	809
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6622	5553	0
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879	5	0
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13	0	10
781	2	0
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1678	5	0
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807	0	5
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57	0	5
297	369	0
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720	22218	0
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69	0	15
3081	10	0
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1766	0	5
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11	0	10
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695	5	0
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24	0	2423
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1751	25	0
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61	3	18
1250	5	0
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6400	0	5
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3934	29488	25802
484	0	10
35	0	30
1453	5	0
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19	1	0
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28	8	0
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189	4	0
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6799	0	4
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96	4	0
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165	0	5
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5	1	0
118	0	1
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684	15	0
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18	2	0
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36	0	2
34696	1	0
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79	8	0
5979	0	4
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315	25	0
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8339	1	0
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11530	3415	3411
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5445	0	1
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8931	1	0
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12	0	2
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4048	1	0
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328	20	0
67	0	8
7905	1	0
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1974	1	0
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2275	0	1
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38	18	0
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11587	0	1
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6577	35	0
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1	7	0
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26	0	20
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16	20	0
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53	0	8
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4073	3377	3377
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49	13	0
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6	25	0
1943	0	1
5064	4	0
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10	3	9
3039	0	1
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1495	1	0
2153	0	6
2904	1	0
6643	9	0
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4	0	8
44	8	0
4	12	0
9505	0	1
2508	1	0
4088	0	1
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21747	4	0
39	28	8
6718	0	1
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8456	0	7
1842	0	4
360	0	1
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15457	1	0
9084	1	0
324	1	0
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764	1	0
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1611	0	3
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3352	1	0
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44	0	5
5639	0	1
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4916	0	1
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77	4	0
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2137	1	0
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656	39668	39663
6347	1	0
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3742	1	0
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85	1	0
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726	1	0
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23825	71166	54470
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75	0	249
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184	0	2
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8	10365	3869
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7241	1	0
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687	1	0
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8	0	2
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3592	1	0
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386	42043	2085
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23	466	6295
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107	75521	109875
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69	0	1
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529	15	0
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571	2867	0
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91	14933	6252
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145	27265426	33888524
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6325	87	0
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22	4	0
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34	0	54
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6	0	1
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12	18	30
19	42	2
24	137	35
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52	156	8
22	57	9
21	5	0
33	1	0
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36	5	0
46	1	0
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64	3	0
27	3	0
57	3	0
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59	17	0
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9	3	0
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27	0	3
61	3	0
15	9	0
78	5	0
95	0	1
50	101	15
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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 347857423 NA18952_chrY 54292867 + 6460401 10168907 HG002_chrY 62432599 - 52562439 56521946 2
17919	0	4
43	1	0
4751	1	0
10500	0	1
8947	2	0
1681	0	5
8239	2	0
3181	0	2
6995	0	1
123	0	12
1799	5	0
2002	1	0
356	2	0
1	11	0
470	1	0
5331	8	0
10376	2	0
8865	1	0
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8902	0	1
4227	4	0
29	2	0
787	0	2
2008	0	121806
153	0	1
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81	2	0
3714	0	1
358	0	1
5812	2	16
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3134	0	4
26	2	0
117	0	1
7025	6	0
497	1	0
1301	0	5
633	0	4
2929	2668	104118
12	0	1
5071	4	0
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375	1	0
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101	2	0
1693	0	5
2000	0	1
358	1	0
3885	1	0
1937	28	0
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22	0	2
121	1	0
6982	0	40601
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26	46	0
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6271	0	1
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43025	0	1
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50	8	0
103	4	0
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3508	0	1
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35	4	0
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44138	1	0
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18460	0	1
4033	16	0
13783	1	0
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3921	3	0
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4730	1	0
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13166	50	0
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454	300	0
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9355	1	0
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2588	6	0
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14228	0	1
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69584	1	0
21522	0	4
11393	0	2
71216	19	26
75	0	8
1640	6	0
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35478	1	0
1400	1	0
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1159	0	10004
4052	8	0
12277	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	2	0
5732	6	0
17684	1602	0
322	0	1
2755	2	0
1755	0	1
3328	34	0
59	2	0
43	0	2
26	0	6
2	2	0
172	8	0
176	0	1
364	0	1
1701	0	1
999	0	2
687	4	0
1023	0	14
306	1	0
1673	0	2
2334	0	1
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32	1	3
886	0	2
320	0	1
375	2	0
2675	20326	0
8061	0	1
285	20	0
569	1	0
1721	0	4
311	0	1
311	1	0
292

chain 3742418 NA18952_chrY 54292867 + 19559529 19599190 HG002_chrY 62432599 - 42850342 42889998 3
8542	0	1
11422	6	0
17025	2	0
881	0	2
1783

chain 2027670 NA18952_chrY 54292867 + 1586971 1608737 HG002_chrY 62432599 + 1390502 1412261 4
84	4	0
334	2	0
397	4	0
311	4	0
53	2	0
152	0	4
229	0	1
328	1	0
77	0	4
374	0	1
127	10	0
2	0	9
321	0	1
27	0	2
75	0	1
45	0	1
61	0	1
105	0	1
82	4	0
704	0	2
220	0	1
200	1	0
337	1	0
13	1	0
147	1	0
126	0	7
368	1	0
56	4	0
1	0	1
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132	1	0
36	0	7
51	0	1
63	0	2
337	0	3
18	0	1
91	1	0
349	0	1
35	0	1
34	2	0
30	3	0
283	1	0
148	1	0
160	0	5
124	0	1
7	0	1
10	0	1
121	1	0
776	3	0
293	3	0
300	3	0
22	1	0
696	1	0
438	0	1
12	0	1
179	0	1
419	3	0
80	5	0
2	0	8
178	4	0
148	2	0
227	1	0
176	0	3
2284	2	0
1059	2	0
216	2	0
3047	0	1
298	1	0
314	4	0
862	1	0
310	0	1
971	0	1
201	0	2
581	2	0
11	1	0
188

chain 1126581 NA18952_chrY 54292867 + 1566402 1578727 HG002_chrY 62432599 + 1369992 1382286 5
405	0	2
66	0	2
107	0	1
171	0	1
126	1	0
76	0	1
387	0	1
82	0	1
14	1	0
195	0	1
419	2	0
27	0	1
13	1	0
268	0	1
344	0	2
198	1	0
398	1	0
97	1	0
97	0	3
95	1	0
297	0	4
46	1	0
94	1	0
183	0	3
82	5	0
68	0	1
329	1	0
16	1	0
59	5	0
4	1	0
150	8	6
75	3	0
92	0	1
137	2	0
463	4	0
7	0	1
312	1	0
88	7	0
46	2	0
5	1	0
118	0	4
71	0	2
632	1	0
161	0	4
156	7	0
14	0	3
176	1	0
153	4	0
40	0	2
250	2	0
6	1	0
932	4	0
289	0	1
247	3	0
4	0	2
88	0	1
885	0	2
332	1	0
83	0	1
200	5	0
204	1	0
138	0	3
345	1	0
31	0	1
10	1	0
54	0	1
158	0	2
72	3	0
31	4	0
2	0	3
137	1	0
7	2	0
43	2	0
22

chain 791803 NA18952_chrY 54292867 + 1541358 1550003 HG002_chrY 62432599 + 1344771 1353426 6
18	0	2
49	0	3
75	0	1
1414	2	0
29	0	2
586	1	0
1072	3	0
187	4	3
10	0	2
198	1	0
98	0	2
263	1	0
200	2	0
28	0	3
125	0	1
43	1	0
139	3	0
3	0	1
206	0	1
51	0	4
235	0	2
114	1	0
17	1	0
212	1	0
176	0	1
42	0	2
240	0	2
203	0	1
44	0	1
111	2	0
102	0	1
33	2	0
54	0	1
172	4	0
187	0	1
2	0	1
70	0	1
2	0	1
74	0	1
2	0	1
702	0	3
123	0	2
99	1	0
175	0	4
1	4	0
94	1	0
399	6	0
125

chain 547618 NA18952_chrY 54292867 + 1408833 1414658 HG002_chrY 62432599 + 1437631 1443449 7
197	4	0
190	4	0
4015	0	1
607	0	1
673	1	0
134

chain 544816 NA18952_chrY 54292867 + 1624921 1630726 HG002_chrY 62432599 + 1428050 1433850 8
516	0	1
160	2	0
8	19	0
54	0	18
1698	4	0
38	0	1
1172	1	0
1779	0	1
354

chain 529069 NA18952_chrY 54292867 + 1581214 1586971 HG002_chrY 62432599 + 1384760 1390498 9
616	1	0
355	0	2
4	0	1
165	1	0
146	1	0
532	2	0
683	1	0
357	4	0
204	4	0
425	1	0
79	1	0
4	3	0
377	0	4
18	2	0
125	0	1
41	1	0
10	1	0
174	1	0
176	23	15
50	0	1
200	0	4
969

chain 427633 NA18952_chrY 54292867 + 23273959 23278470 HG002_chrY 62432599 - 39338719 39343231 10
2490	0	1
2021

chain 409220 NA18952_chrY 54292867 + 1518309 1522789 HG002_chrY 62432599 + 1321545 1326023 11
391	0	1
137	0	1
13	0	1
2	0	1
175	1	0
5	0	3
16	1	0
67	20	0
7	0	18
261	0	3
2	4	0
35	0	1
370	1	0
1281	0	1
3	0	1
121	2	0
100	2	0
3	0	9
31	1	0
155	1	0
146	0	1
9	1	0
81	6	0
24	0	1
87	0	2
644	0	1
166	1	0
20	6	0
81

chain 386141 NA18952_chrY 54292867 + 1610313 1614407 HG002_chrY 62432599 + 1413828 1417921 12
2671	0	1
604	1	0
475	1	0
342

chain 359101 NA18952_chrY 54292867 + 1630728 1634509 HG002_chrY 62432599 + 1433850 1437631 13
3781

chain 339020 NA18952_chrY 54292867 + 1557114 1560838 HG002_chrY 62432599 + 1360739 1364437 14
369	0	2
65	0	1
191	0	1
16	1	0
15	2	0
271	0	1
186	0	1
186	13	0
489	1	0
61	0	1
62	2	0
133	0	1
31	1	0
61	3	0
26	1	0
99	0	5
49	0	1
11	1	0
46	0	1
212	0	2
8	0	1
165	3	0
53	2	0
7	0	2
24	16	0
842

chain 329974 NA18952_chrY 54292867 + 1614419 1617980 HG002_chrY 62432599 + 1417921 1421463 15
170	4	0
63	4	0
318	8	0
186	4	0
205	4	0
37	0	8
64	4	0
1627	1	0
293	0	2
569

chain 322143 NA18952_chrY 54292867 + 14938897 14942309 HG002_chrY 62432599 - 47507067 47510475 16
619	4	0
2789

chain 244172 NA18952_chrY 54292867 + 1538501 1541106 HG002_chrY 62432599 + 1341904 1344515 17
89	0	3
79	0	1
165	0	3
486	0	1
368	1	0
318	2	0
348	0	1
749

chain 242102 NA18952_chrY 54292867 + 1552262 1554884 HG002_chrY 62432599 + 1355906 1358531 18
55	0	1
194	2	0
226	3	0
16	0	1
26	0	1
14	0	5
236	0	3
662	3	0
105	1	0
38	2	0
343	0	4
369	1	0
326

chain 238786 NA18952_chrY 54292867 + 1530948 1533577 HG002_chrY 62432599 + 1334334 1336959 19
439	1	0
355	1	0
64	1	0
27	1	0
3	3	0
38	2	0
45	1	0
203	18	15
397	0	1
261	0	2
2	0	4
166	0	2
163	0	3
408	3	0
27

chain 230453 NA18952_chrY 54292867 + 1578731 1581214 HG002_chrY 62432599 + 1382286 1384756 20
310	1	0
14	0	1
70	1	0
424	0	1
618	1	0
85	4	0
43	1	0
6	4	0
17	3	0
881

chain 224666 NA18952_chrY 54292867 + 1563200 1565644 HG002_chrY 62432599 + 1366814 1369261 21
437	0	2
232	1	0
95	4	0
218	1	0
8	0	1
41	0	1
82	0	1
48	2	0
176	0	1
30	2	0
41	0	2
600	0	2
267	0	3
159

chain 217360 NA18952_chrY 54292867 + 1525157 1527687 HG002_chrY 62432599 + 1328214 1330611 22
6	0	17
66	0	1
6	0	1
10	23	0
18	49	0
5	73	0
114	1	0
8	0	1
1	0	1
180	0	3
1	6	0
127	0	1
67	2	0
428	1	0
791	0	2
4	5	0
538

chain 192423 NA18952_chrY 54292867 + 1534625 1536777 HG002_chrY 62432599 + 1338051 1340200 23
27	0	2
144	0	3
652	1	0
108	0	1
164	1	0
23	2	0
92	8	0
1	0	5
66	6	0
1	0	5
123	1	0
375	1	0
202	1	0
57	0	2
96

chain 172180 NA18952_chrY 54292867 + 1623034 1624897 HG002_chrY 62432599 + 1426185 1428050 24
47	0	1
170	1	0
1167	0	2
478

chain 157877 NA18952_chrY 54292867 + 1523119 1524842 HG002_chrY 62432599 + 1326349 1328070 25
79	1	0
254	2	0
11	0	1
2	2	0
132	1	0
99	0	1
17	0	1
8	0	2
435	4	0
361	0	2
309	0	1
6

chain 146805 NA18952_chrY 54292867 + 1618215 1619799 HG002_chrY 62432599 + 1421686 1423260 26
5	8	0
311	1	0
1250	1	0
8

chain 133054 NA18952_chrY 54292867 + 1555652 1557114 HG002_chrY 62432599 + 1359288 1360738 27
254	1	0
76	0	1
48	1	0
27	2	0
282	6	0
305	3	0
120	1	0
165	0	1
171

chain 123477 NA18952_chrY 54292867 + 1621725 1623033 HG002_chrY 62432599 + 1424876 1426185 28
678	0	1
630

chain 121179 NA18952_chrY 54292867 + 1516590 1517918 HG002_chrY 62432599 + 1319764 1321088 29
119	6	0
297	4	0
180	0	10
21	1	0
74	1	0
213	0	2
385	4	0
23

chain 113098 NA18952_chrY 54292867 + 1515342 1516586 HG002_chrY 62432599 + 1318526 1319764 30
545	0	4
208	1	0
3	1	0
351	4	0
43	4	0
84

chain 106570 NA18952_chrY 54292867 + 1536783 1537941 HG002_chrY 62432599 + 1340200 1341361 31
120	1	0
167	0	1
221	0	1
8	0	2
132	1	0
67	0	2
53	1	0
387

chain 103479 NA18952_chrY 54292867 + 1620305 1621400 HG002_chrY 62432599 + 1423778 1424876 32
499	0	3
596

chain 102989 NA18952_chrY 54292867 + 1551145 1552262 HG002_chrY 62432599 + 1354551 1355671 33
325	0	1
96	0	1
276	0	1
250	0	1
25	1	0
144

chain 98123 NA18952_chrY 54292867 + 1550044 1551142 HG002_chrY 62432599 + 1353457 1354551 34
173	0	7
1	7	0
37	3	0
185	0	1
47	0	1
181	2	0
366	2	0
22	0	2
11	1	0
60

chain 87060 NA18952_chrY 54292867 + 1533678 1534625 HG002_chrY 62432599 + 1337082 1338033 35
252	0	3
269	0	1
10	0	1
240	1	0
175

chain 84252 NA18952_chrY 54292867 + 1609231 1610142 HG002_chrY 62432599 + 1412748 1413655 36
13	3	0
723	1	0
60	0	1
95	1	0
15

chain 77860 NA18952_chrY 54292867 + 1561665 1562522 HG002_chrY 62432599 + 1365266 1366123 37
204	0	1
73	0	6
2	7	0
571

chain 76614 NA18952_chrY 54292867 + 1560840 1561665 HG002_chrY 62432599 + 1364437 1365261 38
20	1	0
15	0	1
2	1	0
786

chain 75963 NA18952_chrY 54292867 + 1527848 1528658 HG002_chrY 62432599 + 1330772 1331582 39
518	0	1
40	1	0
251

chain 66950 NA18952_chrY 54292867 + 1530195 1530940 HG002_chrY 62432599 + 1333076 1334334 40
93	0	518
371	1	0
63	4	0
213

chain 61961 NA18952_chrY 54292867 + 1562522 1563200 HG002_chrY 62432599 + 1366129 1366813 41
315	2	0
2	0	4
14	0	2
208	0	2
137

chain 60940 NA18952_chrY 54292867 + 1514658 1515342 HG002_chrY 62432599 + 1317840 1318522 42
232	4	0
137	0	1
91	6	0
4	0	7
210

chain 59579 NA18952_chrY 54292867 + 1555003 1555644 HG002_chrY 62432599 + 1358648 1359288 43
623	1	0
17

chain 50730 NA18952_chrY 54292867 + 1537963 1538501 HG002_chrY 62432599 + 1341361 1341902 44
504	0	1
12	0	2
22

chain 45451 NA18952_chrY 54292867 + 1608741 1609227 HG002_chrY 62432599 + 1412261 1412748 45
41	0	1
445

chain 39958 NA18952_chrY 54292867 + 1529763 1530187 HG002_chrY 62432599 + 1332652 1333076 46
424

chain 38453 NA18952_chrY 54292867 + 1529098 1529512 HG002_chrY 62432599 + 1331993 1332409 47
383	0	2
31

chain 35051 NA18952_chrY 54292867 + 1517922 1518305 HG002_chrY 62432599 + 1321088 1321469 48
251	2	0
130

chain 30431 NA18952_chrY 54292867 + 1528660 1528984 HG002_chrY 62432599 + 1331582 1331906 49
324

chain 30154 NA18952_chrY 54292867 + 1619977 1620294 HG002_chrY 62432599 + 1423461 1423778 50
317

chain 26088 NA18952_chrY 54292867 + 1565935 1566236 HG002_chrY 62432599 + 1369544 1369842 51
145	4	0
82	0	2
22	1	0
47

chain 25731 NA18952_chrY 54292867 + 1565648 1565927 HG002_chrY 62432599 + 1369261 1369544 52
172	0	4
107

chain 23748 NA18952_chrY 54292867 + 1522789 1523062 HG002_chrY 62432599 + 1326027 1326297 53
108	0	1
26	1	0
48	1	0
11	3	0
60	0	1
15

chain 23470 NA18952_chrY 54292867 + 1541106 1541357 HG002_chrY 62432599 + 1344520 1344771 54
251

chain 22856 NA18952_chrY 54292867 + 1529512 1529751 HG002_chrY 62432599 + 1332413 1332652 55
239

chain 20847 NA18952_chrY 54292867 + 1617980 1618199 HG002_chrY 62432599 + 1421467 1421686 56
219

chain 14901 NA18952_chrY 54292867 + 1610142 1610302 HG002_chrY 62432599 + 1413661 1413821 57
160

chain 14863 NA18952_chrY 54292867 + 1527687 1527847 HG002_chrY 62432599 + 1330612 1330772 58
160

chain 11303 NA18952_chrY 54292867 + 1566240 1566365 HG002_chrY 62432599 + 1369842 1369971 59
57	0	4
68

chain 10156 NA18952_chrY 54292867 + 1554884 1554998 HG002_chrY 62432599 + 1358532 1358648 60
54	0	2
60

chain 8834 NA18952_chrY 54292867 + 1533578 1533678 HG002_chrY 62432599 + 1336964 1337063 61
57	1	0
42

chain 8739 NA18952_chrY 54292867 + 1619870 1619977 HG002_chrY 62432599 + 1423352 1423460 62
48	0	1
42	1	0
12	0	1
4

chain 7488 NA18952_chrY 54292867 + 1528989 1529075 HG002_chrY 62432599 + 1331906 1331993 63
52	0	1
34

chain 4397 NA18952_chrY 54292867 + 1523063 1523111 HG002_chrY 62432599 + 1326297 1326345 64
48

chain 3863 NA18952_chrY 54292867 + 1619800 1619850 HG002_chrY 62432599 + 1423260 1423312 65
35	0	1
1	0	1
14

chain 3706 NA18952_chrY 54292867 + 1524914 1524977 HG002_chrY 62432599 + 1328096 1328170 66
8	0	4
14	0	1
21	0	5
14	0	1
6

chain 2829 NA18952_chrY 54292867 + 1525102 1525136 HG002_chrY 62432599 + 1328179 1328214 67
23	0	1
11

chain 2683 NA18952_chrY 54292867 + 12552570 12552598 HG002_chrY 62432599 + 12511308 12511336 68
28

chain 1956 NA18952_chrY 54292867 + 1566369 1566390 HG002_chrY 62432599 + 1369971 1369992 69
21

chain 1361 NA18952_chrY 54292867 + 1619850 1619866 HG002_chrY 62432599 + 1423316 1423332 70
16

chain 1264 NA18952_chrY 54292867 + 1524874 1524887 HG002_chrY 62432599 + 1328072 1328085 71
13