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sample2_recal_data.table
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sample2_recal_data.table
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#:GATKReport.v1.1:5
#:GATKTable:2:17:%s:%s:;
#:GATKTable:Arguments:Recalibration argument collection values used in this run
Argument Value
binary_tag_name null
covariate ReadGroupCovariate,QualityScoreCovariate,ContextCovariate,CycleCovariate
default_platform null
deletions_default_quality 45
force_platform null
indels_context_size 3
insertions_default_quality 45
low_quality_tail 2
maximum_cycle_value 500
mismatches_context_size 2
mismatches_default_quality -1
no_standard_covs false
quantizing_levels 16
recalibration_report null
run_without_dbsnp false
solid_nocall_strategy THROW_EXCEPTION
solid_recal_mode SET_Q_ZERO
#:GATKTable:3:94:%d:%d:%d:;
#:GATKTable:Quantized:Quality quantization map
QualityScore Count QuantizedScore
0 0 93
1 0 93
2 0 93
3 0 93
4 0 93
5 0 93
6 0 93
7 0 93
8 0 93
9 0 93
10 0 93
11 1531126 11
12 0 12
13 41591995 13
14 0 93
15 0 93
16 0 93
17 0 93
18 0 93
19 0 93
20 0 93
21 0 93
22 0 93
23 0 93
24 0 93
25 0 93
26 0 93
27 0 93
28 0 93
29 0 93
30 0 93
31 0 93
32 0 93
33 0 93
34 0 93
35 0 93
36 0 93
37 0 93
38 0 93
39 0 93
40 0 93
41 0 93
42 0 93
43 0 93
44 0 93
45 0 93
46 0 93
47 0 93
48 0 93
49 0 93
50 0 93
51 0 93
52 0 93
53 0 93
54 0 93
55 0 93
56 0 93
57 0 93
58 0 93
59 0 93
60 0 93
61 0 93
62 0 93
63 0 93
64 0 93
65 0 93
66 0 93
67 0 93
68 0 93
69 0 93
70 0 93
71 0 93
72 0 93
73 0 93
74 0 93
75 0 93
76 0 93
77 0 93
78 0 93
79 0 93
80 0 93
81 0 93
82 0 93
83 0 83
84 0 84
85 0 85
86 0 86
87 0 87
88 0 88
89 0 89
90 0 90
91 0 91
92 0 92
93 0 93
#:GATKTable:6:1:%s:%s:%.4f:%.4f:%d:%.2f:;
#:GATKTable:RecalTable0:
ReadGroup EventType EmpiricalQuality EstimatedQReported Observations Errors
unit1 M 13.0000 25.7839 43123121 2138908.00
#:GATKTable:6:7:%s:%d:%s:%.4f:%d:%.2f:;
#:GATKTable:RecalTable1:
ReadGroup QualityScore EventType EmpiricalQuality Observations Errors
unit1 8 M 11.0000 27208 2191.00
unit1 12 M 11.0000 1503918 133090.00
unit1 22 M 13.0000 1112039 57096.00
unit1 27 M 13.0000 1304571 63999.00
unit1 32 M 13.0000 2254792 105510.00
unit1 37 M 13.0000 5566486 265870.00
unit1 41 M 13.0000 31354107 1511152.00
#:GATKTable:8:1925:%s:%d:%s:%s:%s:%.4f:%d:%.2f:;
#:GATKTable:RecalTable2:
ReadGroup QualityScore CovariateValue CovariateName EventType EmpiricalQuality Observations Errors
unit1 8 -10 Cycle M 8.0000 41 0.00
unit1 8 -100 Cycle M 9.0000 88 1.00
unit1 8 -101 Cycle M 8.0000 90 12.00
unit1 8 -102 Cycle M 8.0000 87 9.00
unit1 8 -103 Cycle M 8.0000 93 8.00
unit1 8 -104 Cycle M 8.0000 86 13.00
unit1 8 -105 Cycle M 8.0000 82 7.00
unit1 8 -106 Cycle M 9.0000 85 3.00
unit1 8 -107 Cycle M 8.0000 87 9.00
unit1 8 -108 Cycle M 8.0000 89 10.00
unit1 8 -109 Cycle M 8.0000 93 6.00
unit1 8 -11 Cycle M 8.0000 48 0.00
unit1 8 -110 Cycle M 8.0000 96 7.00
unit1 8 -111 Cycle M 8.0000 94 7.00
unit1 8 -112 Cycle M 8.0000 101 8.00
unit1 8 -113 Cycle M 8.0000 118 10.00
unit1 8 -114 Cycle M 9.0000 108 5.00
unit1 8 -115 Cycle M 9.0000 108 7.00
unit1 8 -116 Cycle M 8.0000 110 8.00
unit1 8 -117 Cycle M 8.0000 129 16.00
unit1 8 -118 Cycle M 8.0000 126 11.00
unit1 8 -119 Cycle M 8.0000 129 15.00
unit1 8 -12 Cycle M 9.0000 91 0.00
unit1 8 -120 Cycle M 8.0000 153 18.00
unit1 8 -121 Cycle M 9.0000 153 11.00
unit1 8 -122 Cycle M 8.0000 137 13.00
unit1 8 -123 Cycle M 9.0000 145 11.00
unit1 8 -124 Cycle M 9.0000 175 14.00
unit1 8 -125 Cycle M 8.0000 185 20.00
unit1 8 -126 Cycle M 9.0000 182 13.00
unit1 8 -127 Cycle M 8.0000 191 19.00
unit1 8 -128 Cycle M 8.0000 188 20.00
unit1 8 -129 Cycle M 9.0000 1371 151.00
unit1 8 -13 Cycle M 9.0000 102 0.00
unit1 8 -130 Cycle M 9.0000 1316 127.00
unit1 8 -131 Cycle M 10.0000 1227 103.00
unit1 8 -132 Cycle M 9.0000 1344 153.00
unit1 8 -133 Cycle M 10.0000 1614 155.00
unit1 8 -134 Cycle M 10.0000 1338 119.00
unit1 8 -135 Cycle M 10.0000 1239 111.00
unit1 8 -136 Cycle M 9.0000 1182 111.00
unit1 8 -137 Cycle M 10.0000 1187 98.00
unit1 8 -138 Cycle M 10.0000 1055 77.00
unit1 8 -139 Cycle M 10.0000 1216 101.00
unit1 8 -14 Cycle M 9.0000 110 0.00
unit1 8 -140 Cycle M 10.0000 1121 101.00
unit1 8 -15 Cycle M 9.0000 126 0.00
unit1 8 -16 Cycle M 9.0000 122 1.00
unit1 8 -17 Cycle M 9.0000 166 2.00
unit1 8 -18 Cycle M 9.0000 180 2.00
unit1 8 -19 Cycle M 9.0000 172 4.00
unit1 8 -20 Cycle M 9.0000 109 6.00
unit1 8 -21 Cycle M 9.0000 109 6.00
unit1 8 -22 Cycle M 9.0000 109 5.00
unit1 8 -23 Cycle M 8.0000 101 7.00
unit1 8 -24 Cycle M 9.0000 99 4.00
unit1 8 -25 Cycle M 9.0000 89 4.00
unit1 8 -26 Cycle M 8.0000 102 9.00
unit1 8 -27 Cycle M 8.0000 100 6.00
unit1 8 -28 Cycle M 8.0000 94 7.00
unit1 8 -29 Cycle M 9.0000 89 2.00
unit1 8 -30 Cycle M 8.0000 92 9.00
unit1 8 -31 Cycle M 8.0000 92 8.00
unit1 8 -32 Cycle M 8.0000 84 9.00
unit1 8 -33 Cycle M 8.0000 97 7.00
unit1 8 -34 Cycle M 9.0000 98 3.00
unit1 8 -35 Cycle M 8.0000 97 9.00
unit1 8 -36 Cycle M 9.0000 101 5.00
unit1 8 -37 Cycle M 8.0000 100 6.00
unit1 8 -38 Cycle M 9.0000 114 3.00
unit1 8 -39 Cycle M 8.0000 109 9.00
unit1 8 -40 Cycle M 9.0000 118 5.00
unit1 8 -41 Cycle M 8.0000 96 6.00
unit1 8 -42 Cycle M 9.0000 109 6.00
unit1 8 -43 Cycle M 8.0000 85 7.00
unit1 8 -44 Cycle M 9.0000 90 3.00
unit1 8 -45 Cycle M 9.0000 93 4.00
unit1 8 -46 Cycle M 9.0000 104 3.00
unit1 8 -47 Cycle M 8.0000 112 8.00
unit1 8 -48 Cycle M 9.0000 124 8.00
unit1 8 -49 Cycle M 9.0000 112 7.00
unit1 8 -50 Cycle M 9.0000 93 2.00
unit1 8 -51 Cycle M 9.0000 125 8.00
unit1 8 -52 Cycle M 8.0000 100 12.00
unit1 8 -53 Cycle M 8.0000 93 8.00
unit1 8 -54 Cycle M 8.0000 81 7.00
unit1 8 -55 Cycle M 8.0000 87 5.00
unit1 8 -56 Cycle M 9.0000 81 3.00
unit1 8 -57 Cycle M 9.0000 93 4.00
unit1 8 -58 Cycle M 9.0000 83 1.00
unit1 8 -59 Cycle M 8.0000 84 4.00
unit1 8 -60 Cycle M 8.0000 75 4.00
unit1 8 -61 Cycle M 8.0000 83 7.00
unit1 8 -62 Cycle M 9.0000 89 2.00
unit1 8 -63 Cycle M 8.0000 80 6.00
unit1 8 -64 Cycle M 8.0000 79 4.00
unit1 8 -65 Cycle M 8.0000 77 6.00
unit1 8 -66 Cycle M 8.0000 73 3.00
unit1 8 -67 Cycle M 8.0000 74 10.00
unit1 8 -68 Cycle M 8.0000 76 6.00
unit1 8 -69 Cycle M 8.0000 87 5.00
unit1 8 -70 Cycle M 8.0000 76 5.00
unit1 8 -71 Cycle M 9.0000 73 2.00
unit1 8 -72 Cycle M 8.0000 88 6.00
unit1 8 -73 Cycle M 8.0000 73 6.00
unit1 8 -74 Cycle M 9.0000 73 2.00
unit1 8 -75 Cycle M 8.0000 82 8.00
unit1 8 -76 Cycle M 8.0000 69 2.00
unit1 8 -77 Cycle M 8.0000 80 6.00
unit1 8 -78 Cycle M 9.0000 93 4.00
unit1 8 -79 Cycle M 8.0000 75 3.00
unit1 8 -8 Cycle M 8.0000 15 0.00
unit1 8 -80 Cycle M 8.0000 91 5.00
unit1 8 -81 Cycle M 8.0000 77 12.00
unit1 8 -82 Cycle M 8.0000 98 7.00
unit1 8 -83 Cycle M 8.0000 103 7.00
unit1 8 -84 Cycle M 8.0000 114 9.00
unit1 8 -85 Cycle M 8.0000 94 6.00
unit1 8 -86 Cycle M 8.0000 101 8.00
unit1 8 -87 Cycle M 8.0000 86 7.00
unit1 8 -88 Cycle M 8.0000 82 6.00
unit1 8 -89 Cycle M 9.0000 83 3.00
unit1 8 -9 Cycle M 8.0000 31 0.00
unit1 8 -90 Cycle M 8.0000 93 11.00
unit1 8 -91 Cycle M 8.0000 102 8.00
unit1 8 -92 Cycle M 8.0000 88 5.00
unit1 8 -93 Cycle M 8.0000 88 6.00
unit1 8 -94 Cycle M 8.0000 79 8.00
unit1 8 -95 Cycle M 9.0000 89 4.00
unit1 8 -96 Cycle M 8.0000 65 2.00
unit1 8 -97 Cycle M 8.0000 77 5.00
unit1 8 -98 Cycle M 8.0000 85 10.00
unit1 8 -99 Cycle M 8.0000 68 3.00
unit1 8 AA Context M 9.0000 244 10.00
unit1 8 AC Context M 10.0000 1148 104.00
unit1 8 AG Context M 11.0000 1882 119.00
unit1 8 AT Context M 9.0000 300 13.00
unit1 8 CA Context M 11.0000 2498 130.00
unit1 8 CC Context M 9.0000 3356 360.00
unit1 8 CG Context M 6.0000 1101 306.00
unit1 8 CT Context M 12.0000 2884 97.00
unit1 8 GA Context M 12.0000 2267 99.00
unit1 8 GC Context M 10.0000 2888 223.00
unit1 8 GG Context M 9.0000 2973 403.00
unit1 8 GT Context M 11.0000 1962 119.00
unit1 8 TA Context M 9.0000 152 13.00
unit1 8 TC Context M 11.0000 1388 83.00
unit1 8 TG Context M 11.0000 1923 97.00
unit1 8 TT Context M 9.0000 242 15.00
unit1 12 -1 Cycle M 13.0000 10361 457.00
unit1 12 -10 Cycle M 12.0000 8854 535.00
unit1 12 -100 Cycle M 10.0000 5584 605.00
unit1 12 -101 Cycle M 10.0000 5847 617.00
unit1 12 -102 Cycle M 10.0000 5322 600.00
unit1 12 -103 Cycle M 10.0000 5974 657.00
unit1 12 -104 Cycle M 10.0000 4748 462.00
unit1 12 -105 Cycle M 10.0000 6253 710.00
unit1 12 -106 Cycle M 10.0000 5563 523.00
unit1 12 -107 Cycle M 10.0000 5207 516.00
unit1 12 -108 Cycle M 10.0000 6047 610.00
unit1 12 -109 Cycle M 10.0000 5469 557.00
unit1 12 -11 Cycle M 11.0000 10304 905.00
unit1 12 -110 Cycle M 11.0000 5157 458.00
unit1 12 -111 Cycle M 11.0000 4799 446.00
unit1 12 -112 Cycle M 11.0000 4832 399.00
unit1 12 -113 Cycle M 11.0000 4528 396.00
unit1 12 -114 Cycle M 10.0000 4827 473.00
unit1 12 -115 Cycle M 10.0000 5237 530.00
unit1 12 -116 Cycle M 11.0000 4635 371.00
unit1 12 -117 Cycle M 11.0000 4419 363.00
unit1 12 -118 Cycle M 11.0000 4303 391.00
unit1 12 -119 Cycle M 10.0000 5483 563.00
unit1 12 -12 Cycle M 11.0000 9694 782.00
unit1 12 -120 Cycle M 11.0000 4546 379.00
unit1 12 -121 Cycle M 11.0000 4292 335.00
unit1 12 -122 Cycle M 11.0000 4993 365.00
unit1 12 -123 Cycle M 11.0000 5158 401.00
unit1 12 -124 Cycle M 12.0000 5104 356.00
unit1 12 -125 Cycle M 11.0000 4915 395.00
unit1 12 -126 Cycle M 11.0000 5686 454.00
unit1 12 -127 Cycle M 12.0000 4916 325.00
unit1 12 -128 Cycle M 11.0000 6027 545.00
unit1 12 -129 Cycle M 12.0000 4323 281.00
unit1 12 -13 Cycle M 11.0000 10051 756.00
unit1 12 -130 Cycle M 12.0000 4168 243.00
unit1 12 -131 Cycle M 12.0000 3936 217.00
unit1 12 -132 Cycle M 12.0000 4166 232.00
unit1 12 -133 Cycle M 11.0000 4849 372.00
unit1 12 -134 Cycle M 12.0000 4226 247.00
unit1 12 -135 Cycle M 13.0000 4326 210.00
unit1 12 -136 Cycle M 13.0000 3879 164.00
unit1 12 -137 Cycle M 13.0000 3813 186.00
unit1 12 -138 Cycle M 13.0000 3764 174.00
unit1 12 -139 Cycle M 12.0000 3915 226.00
unit1 12 -14 Cycle M 12.0000 9108 645.00
unit1 12 -140 Cycle M 13.0000 3795 199.00
unit1 12 -15 Cycle M 12.0000 9233 623.00
unit1 12 -16 Cycle M 11.0000 10178 800.00
unit1 12 -17 Cycle M 12.0000 9623 665.00
unit1 12 -18 Cycle M 11.0000 9271 675.00
unit1 12 -19 Cycle M 12.0000 9604 683.00
unit1 12 -2 Cycle M 15.0000 9259 246.00
unit1 12 -20 Cycle M 10.0000 9201 876.00
unit1 12 -21 Cycle M 10.0000 7920 734.00
unit1 12 -22 Cycle M 10.0000 8396 900.00
unit1 12 -23 Cycle M 9.0000 9666 1247.00
unit1 12 -24 Cycle M 10.0000 8211 861.00
unit1 12 -25 Cycle M 10.0000 7879 829.00
unit1 12 -26 Cycle M 10.0000 7486 787.00
unit1 12 -27 Cycle M 10.0000 7683 756.00
unit1 12 -28 Cycle M 8.0000 13569 1996.00
unit1 12 -29 Cycle M 10.0000 8281 857.00
unit1 12 -3 Cycle M 17.0000 7935 99.00
unit1 12 -30 Cycle M 10.0000 7915 845.00
unit1 12 -31 Cycle M 10.0000 7735 799.00
unit1 12 -32 Cycle M 10.0000 7596 798.00
unit1 12 -33 Cycle M 9.0000 9259 1087.00
unit1 12 -34 Cycle M 9.0000 9212 1112.00
unit1 12 -35 Cycle M 9.0000 9063 1102.00
unit1 12 -36 Cycle M 10.0000 7471 842.00
unit1 12 -37 Cycle M 10.0000 7660 807.00
unit1 12 -38 Cycle M 9.0000 8810 1253.00
unit1 12 -39 Cycle M 10.0000 7680 874.00
unit1 12 -4 Cycle M 15.0000 9677 285.00
unit1 12 -40 Cycle M 10.0000 7338 734.00
unit1 12 -41 Cycle M 10.0000 7086 776.00
unit1 12 -42 Cycle M 10.0000 6432 706.00
unit1 12 -43 Cycle M 9.0000 8602 1184.00
unit1 12 -44 Cycle M 10.0000 7116 811.00
unit1 12 -45 Cycle M 9.0000 7142 850.00
unit1 12 -46 Cycle M 9.0000 7974 1019.00
unit1 12 -47 Cycle M 10.0000 6751 756.00
unit1 12 -48 Cycle M 9.0000 8351 1169.00
unit1 12 -49 Cycle M 10.0000 6698 721.00
unit1 12 -5 Cycle M 15.0000 8879 237.00
unit1 12 -50 Cycle M 10.0000 6369 656.00
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unit1 12 -52 Cycle M 10.0000 6611 676.00
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