##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 2367147547 HG00673_chrY 48804764 + 517 48799152 HG002_chrY 62432599 + 26 62432577 1
92	167	22
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300	0	1
1176	4	0
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20	0	10
107	0	2
55	21	0
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69	29	0
21	8	0
79	29	0
58	0	8
8	4	0
106	132	3
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344	2	0
178	2	0
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18	4	0
669	0	1
341	0	4
1292	0	1
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2036	1	0
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5720	3	0
490	0	1
76	0	2
359	56	0
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831	2	0
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112	0	4
854	24	0
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1	13	0
6	10	0
107	2	0
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1025	0	4
1735	1	0
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824	1	0
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17	0	27
7	40	0
2088	4	0
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2532	0	1
68	1	0
3959	1	0
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6743	1	0
3035	308	0
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73	0	4
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87	4	0
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31	0	1
658	0	1
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39	8	0
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27	60	0
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41	8	0
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60	494	0
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7	155	0
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68	0	4
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581	6	0
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2611	0	2
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2240	318	0
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325	2	0
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26	1	139
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6	0	1
849	0	2
2271	343	0
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315	1	0
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41	0	26
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5	38	0
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21	55	0
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56	120	0
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39	385	388
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98	16	425
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21	172	169
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74	1	0
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8	0	5
8	0	8
182	0	62
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76	1	0
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588	1	0
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11	27	10
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9	30	11
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19	1	0
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65	15	0
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5827	0	1
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25	0	75
631	225	0
119	50	0
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12943	2	0
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4232	2	0
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56	20	0
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22	2	0
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77	10	0
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86	16	0
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80	9	0
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8	0	4
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30	3	9
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10	18	0
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5675	0	3
4	0	20265
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96	4	0
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36	0	6
830	1	0
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1937	0	1
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1	2	0
356	1	0
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1693	2	0
103	0	6
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112	2	0
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43	0	40601
6982	1	0
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22	4	0
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1794	2	0
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26	4	0
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783	32	0
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108	6	0
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20	4	0
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26	0	1
73	0	10
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5	0	12
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32	4	0
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35	4	0
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26	0	4
842	0	1
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31	2	0
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37	0	121774
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24	24	0
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97	0	2
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14	0	4
6	0	2
18	0	6
846	1	0
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1	2	0
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45	0	1
54	0	12
123	0	1
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52	0	8
1672	1	0
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43	0	4
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46582	1006570	326879
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129	11758	50484
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343	46499	156525
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136	1	0
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339	0	20
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2003	0	5
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2014	11383	0
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2013	5	0
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7477	1	0
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39	8	0
4	2	0
6	14	0
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8914	7	0
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13839	1	0
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693	0	4
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56	4	0
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562	1	0
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922	1	0
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328	16	0
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5633	4	0
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930	2	0
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5367	1	0
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5704	2	0
42	23	17
4634	6	0
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991	0	3
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67	0	2
7	0	2
2283	0	1
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8096	0	4
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72	1	0
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17	0	4
5	0	4
105	0	4
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70	0	4
8	0	1
52	4	0
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1082	2	0
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13	0	5
14956	1	0
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379	0	6
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30	2	0
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3569	2	0
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73	19	0
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14	0	1
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80	0	2
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613	0	4
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1734	8	0
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36	0	28
1952	8	0
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32	6	0
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4070	3386	3386
2125	3	0
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3699	1	0
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916	1	0
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6	3	0
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9	1	0
10	12	1
2579	0	2
7039	25	0
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59	3	0
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1	2	0
17806	3457	3457
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6	25	0
9557	0	2
12	0	1
3047	1	0
942	2	0
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5063	1	0
6637	0	6
2857	0	4
2030	1	0
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44	8	0
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3128	1	0
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38	0	3
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86	1	0
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24	0	2
3742	1	0
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726	1	0
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328	1	0
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6034	44729	29501
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78	0	1
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11257	2	0
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145	875	0
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3303	587	1212
52	12434	16432
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64	1	0
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32	4	0
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51	4	2
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438	0	1
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1	8	0
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162	210508	210250
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3592	1	0
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254	0	1
16	36	0
97	1	0
234	0	2
27	0	1
33	4	0
1	0	5
121	2	0
25	1	0
73	0	1
50	4600	2764
121	12	0
77	12	0
117	4	0
176	0	1
95	8	0
91	0	3
210	6	0
2	0	8
75	0	8
117	0	15
117	1	0
31	0	3
197	0	1
107	75534	109875
386	0	3
114	0	2
53	32	0
4	0	28
67	0	1
218	0	7
25	2	0
72	0	2
50	0	3
53	1	0
28	9	0
20	5	0
3	7	0
69	1	0
111	0	2
104	14	0
315	1	0
48	0	2
5	0	1
9	12	0
72	0	1
131	0	2
61	0	6
22	0	2
5	0	152
200	0	1
40	1	0
288	4	0
158	1	0
5	3	0
69	0	1
79	0	5
69	2	0
120	0	3
15	1	0
147	0	3
211	0	14
2	0	4
4	1	0
20	2	0
94	0	2
113	0	8513
18068	1	0
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2002	0	1
4612	0	3
5451	0	2
12445	0	4
64	16	0
216	1	0
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6735	0	2
5079	1	0
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909	10	19
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625	3	0
105	0	1
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22	0	1
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611	1	0
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7889	1	0
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600	1	0
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9971	1	0
2576	1	0
28	0	5
219	9343	1765282
347	0	1
156	0	1
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128	1	0
42	0	1
274	1	0
291	1	0
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81	1	0
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387	1	0
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68	0	1
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61	1	0
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146	0	1
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456	1	0
108	1	0
391	1	0
177	0	1
635	1	0
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28	0	1
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348	0	1
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234	0	1
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320	408	2792
1656	0	1
435	4769	0
7626	1	0
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84	4	0
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100	4	0
17	4	0
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75	0	4
2483	1	0
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4725	4	0
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2055	1	0
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407	0	2
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14	4	0
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4854	0	1
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34	0	2
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21	0	8
4369	3	0
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1859	0	4
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31793	1	0
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29	0	4
41	4	0
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411	2893	0
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324	5	0
414	0	5
506	15	0
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542	0	10
70	0	1
2240	15	0
558	0	10
54	0	1
1760	5	0
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3423	0	10
67	0	1
1002	20	0
332	5	0
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8	0	2878
2264	0	1
601	20	0
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532	10	0
64	1	0
400	0	1
601	20	0
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502	0	10
533	5	0
16	5	0
61	1	0
400	0	1
1869	10	0
1792	0	10
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532	10	0
64	1	0
400	0	1
1359	0	5
505	5	0
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2306	20	0
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465	1	0
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538	0	10
468	1	0
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2883	20	0
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540	0	10
473	1	0
598	0	20
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1248	5	0
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1002	20	0
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60	0	1
1002	20	0
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547	10	0
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496	10	0
622	1	0
3889	20	0
2873	20	0
1771	2873	0
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8	2863	0
2342	15	0
523	0	10
1128	24927	7938
173	1	0
2740	0	5
3410	0	15
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5689	10	0
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40	0	5
12423	5	0
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2801	0	5
18390	3101	0
155	5	0
163	0	12442
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24	20	0
571	10	0
290	5	0
914	0	1
479	0	1
241	10	0
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79	1	0
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565	1	0
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153	5	0
1363	0	1
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914	0	1
586	3127	0
3785	0	5
623	0	10
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4638	1	0
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307	5	0
1781	0	5
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2463	0	3146
7840	8162	2649
6	0	5
10	0	280
5902	0	2763
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420	0	1
2005	0	5
564	5	0
131	30	0
2200	2	0
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700	0	20
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335	10	0
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488	30	0
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1770	20	0
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320	5	0
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47	0	1
156	0	1
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774	0	5
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998	5	0
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3681	5	0
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85	0	1
2263	14717	17471
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291	1	0
253	16548	4
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14551	1204085	1140961
40	3554	0
1932	0	1
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54	0	5
8	26666	33810
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3290	15	0
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7220	0	3554
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4963	51483	22445
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8430	5660	5645
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8128	5	0
6408	21282	0
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393	0	5
672	1	0
684	0	3539
527	1	0
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354	3581	3
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427	0	5
1237	10	0
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1274	15	0
1318	0	5
2130	1	0
44	10	0
810	19538769	32045929
5521	5	0
39	0	290
308	0	3559
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3603	5	0
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1775	40	0
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3	25	0
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13729	17430	2913
3225	0	16
2311	4823	7243
1962	2753	14841
6922	0	2
1	2422	0
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600	1	0
690	2417	0
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5660	40523	38068
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51	1	0
1303	0	4494
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2519	0	7
8	24041	2767
34	0	10
1772	0	5
478	1	0
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3491	944	4478
22	0	10
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35287	1	42398
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2243	0	1
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3534	0	1
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179	5	0
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91	16	16
393	0	5
156	45	0
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583	0	5
150	1	0
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88	15	0
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168	45	0
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103	1	0
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7086	0	15
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2045	1	0
671	0	7095
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215	0	21200
7858	1	0
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74	0	25
14	5122	26107
29526	0	3514
45	0	155
114	0	3609
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24	15	0
371	5	0
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552	30	0
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1984	5	0
6204	28510	10994
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32709	5	0
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115	0	12
3321	0	1
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2765	0	9
10983	0	3
16383	6	0
37980	2	0
12789	0	36
5539	2	0
4328	6	0
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2550	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
3695	0	1
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45	0	6
11	0	3
2374	1	0
4546	0	1
401	0	1
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7219	1	0
4828	1	0
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8900	1	0
658	16	0
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4018	1	0
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6451	0	1
343	0	2
4828	0	1
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530	2	0
2613	1	0
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6099	0	1
73	13	0
272	0	2
2724	2	0
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9625	1	0
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73	0	1
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1366	0	1
1509	2	0
347	0	3
255	3	0
11013	1	0
168	0	1
782	1	0
4759	6	0
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5431	0	12
7985	29	0
27	0	58
687	6	0
106	6	0
193	1	0
52	0	10
1	0	2
43	0	1
10	0	1
15	2	0
3	0	1
83	1	0
20	5	0
18	0	5
12	0	1
12	13	1
42	73	13
19	150	35
21	7	0
7	18	0
2	0	2
12	0	2
17	21	3
17	31	3
12	30	14
48	6	0
43	4	0
7	0	2
6	23	9
53	160	7
22	57	9
21	5	0
33	1	0
8	6	0
36	5	0
46	1	0
1	20	0
15	3	0
64	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
61	3	0
15	9	0
22	0	1
55	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	1666	1
56	0	5
53

chain 178452941 HG00673_chrY_random0000109 2179201 + 411 1915628 HG002_chrY 62432599 - 36872384 38778093 2
119	1	0
54	1	0
105	1	0
132	0	1
79	1	0
401	4	0
209	0	1
15	1	0
558	1	0
76	0	1
186	0	1
9936	4	0
4132	3	0
741	1	0
926	6	0
2474	0	1
1669	1	0
13738	1	0
24854	0	17
15177	1	0
4358	3	0
16550	1	0
27476	0	1
37691	0	1
4082	1	0
6677	0	2
11258	0	1
18593	0	2
4649	8	0
6317	1	0
19246	1	0
40212	0	1
7542	6	0
3490	2	0
2223	0	1
31634	0	2
14599	0	1
1442	0	3
7950	5	0
6	0	3
17309	0	2
12072	0	2
18662	0	1
11218	0	2
21405	1	0
19340	12	0
25	4	0
3983	0	3
9942	0	1
31793	0	8
22513	0	4
9790	2	0
1025	1	0
15556	1	0
10182	0	2
4371	6	0
4	4	0
15	2	0
477	0	6
3377	0	1
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14412	0	1
913	0	2
20379	0	1
10190	1	0
3988	3	0
37815	0	1
1848	6	0
667	2	0
19640	12	0
4262	1	0
15691	1	0
12012	0	4
34	0	12
15548	2	0
2718	27	0
49	0	15
61	0	3
9195	0	6
9997	0	1
922	0	1
11500	0	1
3807	1	0
3054	1	0
3263	0	1
821	0	1
13755	0	5
20593	1	0
1428	1	0
893	1	0
10817	1	0
1868	0	8
5201	10	0
2634	0	3
4705	0	1
904	1	0
1737	8	0
366	1	0
4858	2	0
14	2	0
42244	0	2
24502	4	0
2710	4	0
7193	0	2
2302	1	0
14601	1	0
2705	1	0
214	0	2
4862	0	1
2202	0	1
5060	4	0
9159	1	0
13519	0	1
2051	0	26
5193	0	2
2815	1	0
3805	0	1
1708	1	0
5227	1	0
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4341	0	6
2857	0	7
6645	1	0
1017	0	1
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194	4	0
1453	0	1
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530	4	0
7682	1	0
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4301	0	2
1436	14	0
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13643	0	2
710	2	0
16455	4	0
3835	1	0
2415	1	0
4982	1	0
3060	0	2
28776	4	0
814	0	1
7681	0	2
2173	1	0
6792	1	0
5106	0	1
25772	1	0
7973	1	0
12562	1	0
27964	0	11
9957	4	0
15493	18	0
49302	1	0
2158	1	0
3275	0	2
34118	0	8
126	4	0
8	4	0
104	4	8
3388	0	4
3361	0	5
42733	4	0
1679	0	12
4110	0	4
12156	1	0
5218	1	0
1219	8	0
5357	0	1
17600	0	1
2368	0	1
2244	4770	0
15748	10848	0
18999	1	0
17833	0	10850
4459	1	0
15121	0	4757
158	1	0
435	9570	57
14061	0	1
1568	0	1
3817	0	8
3214	2	0
6077	3	0
9259	0	8
5783	8	0
6200	0	1
3438	12	0
33123	0	6
3387	0	4
3330	4	0
35	4	0
57	0	8
89	4	0
34	4	0
78	0	8
1952	1	0
25243	2	0
12354	0	1
64806	0	16
15793	1	0
600	0	2
6682	0	1
7883	0	8
27475	1	0
30889	0	1
8970	0	1
8498	4	0
20417

chain 427559 HG00673_chrY 48804764 + 23749830 23754341 HG002_chrY 62432599 - 39338719 39343231 3
2490	0	1
2021

chain 327277 HG00673_chrY 48804764 + 19295188 19298645 HG002_chrY 62432599 - 43575590 43579047 4
3457

chain 320916 HG00673_chrY 48804764 + 15363485 15366881 HG002_chrY 62432599 - 47507067 47510475 5
619	0	12
2777