##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 2295268055 HG00290_chrY 58868509 + 29 28338371 HG002_chrY 62432599 + 27 29422110 1
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823	1	0
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220	0	4
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645	2	0
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1831	1	0
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70	104	280
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9	50	14269
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889	18	0
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8	36	0
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20	1	0
70	3	0
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932	0	1
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19	0	3
58	0	1
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791	0	2
689	1	0
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17	0	4
14	0	2
539	0	2
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503	5	0
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1799	0	1
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859	1	0
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167	0	8
548	0	22
18	0	4
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38	4	0
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2174	4	0
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110	1	0
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33	0	4
212	0	4
1093	1	0
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281	0	4
623	0	1
51	0	121
97	41	0
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24	8	0
564	0	1
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772	12	23
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704	1	0
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36	1	0
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47	1	0
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63	1	0
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37	0	1
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4	2	17
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1	153	0
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4	4	3
15	52	12
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15	1	0
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1527	6	0
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8	8	73
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31	1	36
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8	1	0
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6	1	0
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1	0	7
20	0	62
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20	13	66
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31	16	121
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199	1	0
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63	14	0
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2532	16	2
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48	262	0
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72	8	0
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1	5	0
134	0	8
1677	1	0
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42	0	20
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34	0	20
79	15	7
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2	3	0
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7	8	33
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9	1	0
4	7	26
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4	0	2
19	0	1
47	10	27
14	1	0
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8	1	0
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5	0	1
4	0	39
69	3	0
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1926	1	0
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73	0	10
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5	0	18
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13	0	20277
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24	30	0
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2	388	0
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1473	0	4
3934	1	0
2518	0	4
203	0	8
18753	0	1
51756	0	1
11641	0	2
1129	0	3
10276	1	0
14090	4	0
73	19	0
1631	1	0
23827	0	1
8008	0	1
17517	1	0
1524	5	0
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3074	0	1
7311	0	2
272	2	0
19	0	2
4579	1	0
29870	0	1
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14	0	1
2033	2	0
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29	0	2
32276	0	4
11612	0	2
17528	1	0
3557	0	3
6755	0	1
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2345	2	0
6447	0	8
7860	1	0
4562	0	8
13355	0	2
70	0	20
5147	16	0
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961	0	13
17840	4	0
88	4	0
616	0	4
24119	4	0
32	0	2
1222	0	2
318	0	1
207	12	0
107	0	1
80	0	1
178	0	1
31010	0	2
16976	1	0
66	0	1
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434	0	4
7590	1	0
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7980	0	5
3354	0	2
1506	1	0
9213	1	0
2428	3	0
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1402	1	0
6698	0	2
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1652	1	0
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30398	1	0
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11	0	6
5576	1	0
6725	0	3
1	0	1
4	0	4
27342	1	0
3498	0	1
5641	0	1
2512	1	0
9544	8	0
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2252	1	0
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32	4	0
6936	3379	3379
2124	6	0
9919	1	0
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916	1	0
1529	4	0
1476	0	2
46	2	0
9572	25	0
6	4	0
10120	12	0
20	0	1
38	3	0
47	8	0
1	2	0
17806	3457	3457
17809	4	0
50	4	0
59	14	0
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2549	0	2
12	0	1
1498	0	16
1533	1	0
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305	2	0
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4	12	0
9504	0	2
1330	2	0
1178	1	0
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1540	1	0
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8	7	0
6718	0	1
5579	0	4
8	0	8
19131	0	1
7311	1	0
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9432	0	1
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6711	0	1
4399	0	12
15459	1	0
602	1	0
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5622	8	0
57	2	0
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4360	0	8
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102	0	2
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77	4	0
8037	0	28
644	39671	39663
604	0	12
8091	2	0
83	2	0
14790	0	2
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3603	1	0
1312	0	1
86	1	0
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840	1	0
6066	1	0
27	18	0
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649	0	2
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45	0	2
6404	10	0
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5622	0	8
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16	6	27
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23	0	2
1800	1	0
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21	3	31
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3959	1	0
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42	6	0
568	0	8
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5	20	0
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5076	0	3
21	1	0
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880	1	0
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32	2	0
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5945	0	1
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6895	0	1
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472	3	0
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874	0	1
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87	0	1
2739	2	0
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28082	125	0
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667	0	125
159	4	0
336	0	754
724	1	0
2286	5513	0
341	0	2759
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20986	88230	25206
405	1	0
713	0	1
65	4	0
111	251	0
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8073	0	366
6097	1	0
6	0	1
7	1	0
46	0	3980
52	0	747
187	0	1371
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4	1	0
35	2	0
97	0	250
267	42124	29541
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78	0	1
130	0	1
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115	4	0
3	0	3
11257	2	0
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55	214	339
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2	7	0
202	0	125
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209	0	125
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55	0	125
127	0	2872
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145	875	0
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119	2	1876
390	0	125
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332	0	7
3	7	0
240	124	0
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74761	94478	326
9540	4	0
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76	0	12
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7	3	0
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386	42046	2085
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23	466	6295
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121	2	0
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50	4600	2764
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75	0	8
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107	75530	109875
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2260	10	0
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2265	5	0
3886	0	1
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495	0	15
547	0	10
466	0	1
601	5	0
13	17	2
723	0	5
500	0	10
1023	0	1
601	20	0
332	5	0
901	10	0
548	0	10
1084	0	2878
1241	15	0
1792	0	10
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532	10	0
64	1	0
400	0	1
601	20	0
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506	0	5
611	1	0
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2932	1	0
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558	0	10
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510	5	0
558	10	0
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1740	0	5
1062	10	0
1068	20	0
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547	10	0
65	0	1
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552	10	0
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547	10	0
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2868	5	0
622	1	0
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2870	20	0
2873	20	0
1771	2873	0
2890	10	0
8	2863	0
2342	15	0
523	0	10
1128	24008	3872
3848	5	0
8986	0	20
5917	0	351
31	5	0
39	15	0
8	9	0
19	0	21
9	19	0
59	1	0
12	10	0
17	5	0
69	0	35
15	0	14
36	5	0
14	0	5
53	0	10
54	0	65
200	10	0
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472	0	10
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40	0	5
12423	0	5
21751	0	5
18390	3101	0
155	5	0
123	10	0
202	15	0
227	1	0
954	0	1
1579	0	6216
173	5	0
9363	5	0
3089	5	0
4508	0	6197
263	0	10
538	0	5
623	0	10
1202	1	0
474	1	0
253	0	10
1330	5	0
232	0	1
2864	5	0
176	0	15
875	0	1
480	0	1
105	3092	0
148	0	12407
3835	1	0
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2895	5	0
2856	0	10
3221	5	0
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16098	2474	0
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2804	0	5
3328	5	0
131	20	0
33	0	1
1985	0	15
20	10	0
146	2	0
532	30	0
2734	20	0
2003	0	5
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79	1	0
156	1	0
2179	15	0
355	0	20
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47	0	1
156	0	1
783	5	0
435	0	5
965	0	15
306	10	0
26	10	0
61	1	0
1024	0	2764
1656	15	0
73	1	0
2681	5	0
1000	0	5
1758	0	10
3759	5	0
1745	0	5
85	0	1
2263	16938	16943
58	0	5
975	0	10
3159	0	10
1339	5	0
13	0	10
544	8271	4
2590	10	0
25177	7088	7088
13915	0	5
2529	1204336	1140961
40	3559	0
1932	0	1
105	0	5
18	0	5
1966	0	15
1512	0	5
8	6615	24397
10100	1	0
300	0	5
7	0	10
3290	15	0
10772	0	5
7084	5	0
1	10	0
2464	0	7070
379	15	0
691	5	0
1878	5	0
6468	3526	3536
2220	0	7053
3700	0	3554
8344	15613	5937
4977	2	0
273	0	2
1040	57316	52315
4233	0	15
490	0	1
429	0	7121
2624	0	5
918	0	5
1237	10	0
1361	15	0
2211	15	0
2270	5	0
1183	1	0
44	10	0
810	32270	25172
1146	0	5
6349	2411	2411
8561	10363	5513
1070	0	2
5148	0	2416
2574	4979	0
17962	0	1
8017	22199	12689
4310	8616	8616
12057	3534	0
7335	0	5
2414

chain 62071967 HG00290_chrY 58868509 + 58194091 58863833 HG002_chrY 62432599 + 61667243 62432577 2
791	0	2414
392	1	0
1752	5	0
1166	1	0
1035	0	7
199	5	0
656	1	0
1382	0	2414
15	0	1317
1	0	3505
110	2	0
244	0	2
2167	0	2
2285	0	3
9543	1	42398
1075	0	15
2243	0	1
1660	10	0
9	30	0
1042	0	1
442	15	0
380	1	0
1276	0	15
2243	0	1
7068	0	1
2720	0	10604
9169	15	0
24645	0	25
3519	25	0
5416	1	0
1584	0	1
7722	0	7080
15224	40	0
1849	25	0
1644	40	0
1686	0	15
1233	1	0
494	0	20
120	3488	14047
6347	10	0
3555	0	1
513	20	0
61	40	0
21668	10	0
32802	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	14027
3469	5	0
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153	0	8
3325	0	1
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2765	0	6
314	0	1
10671	0	3
9579	1	0
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37980	2	0
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4328	4	0
10053	1	0
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1776	0	3
1309	1	0
724	0	1
1972	4	0
1725	5	0
866	1	0
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7336	0	1
8120	0	5
407	1	0
1864	6	0
7215	0	1
3912	0	4
915	0	3
3142	16	0
8900	1	0
658	0	32
74	80	0
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343	0	2
4828	0	1
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27	58	0
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27	24	0
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20	25	182
14	0	6
3	2	0
10	0	54
6	0	1
19	0	1
17	20	46
24	135	29
21	34	13
16	0	1
18	21	3
17	10	0
3	1	0
12	14	4
9	1	0
1	5	0
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18	0	17
3	0	1
29	0	1
15	4	0
7	0	2
6	23	9
28	0	1
24	4	0
9	0	1
19	51	9
9	0	5
16	1	0
14	0	12
42	5	0
6	0	1
21	0	7
12	20	0
15	3	0
44	18	20
27	3	0
57	3	0
21	3	0
59	64	23
27	0	3
33	1	43
15	5	214
13	0	32
57	2	0
29	4	0
66	0	1
1	0	37
12	0	1
22	4	0
70	4	0
4	0	6
20	0	1
29	0	1
6	764	1
51	0	10
19	3	0
34

chain 3742797 HG00290_chrY 58868509 + 20006188 20045852 HG002_chrY 62432599 - 42850342 42889998 3
19965	4	0
17025	4	0
2666

chain 427764 HG00290_chrY 58868509 + 23798397 23802908 HG002_chrY 62432599 - 39338719 39343231 4
2490	0	1
2021

chain 327277 HG00290_chrY 58868509 + 19317053 19320510 HG002_chrY 62432599 - 43575590 43579047 5
3457

chain 1446 HG00290_chrY 58868509 + 58865275 58865290 HG002_chrY 62432599 + 62432584 62432599 6
15