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1 ## net.sf.picard.metrics.StringHeader
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2 # net.sf.picard.analysis.CollectGcBiasMetrics REFERENCE_SEQUENCE=testdata/picard/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta INPUT=testdata/picard/sam/summary_alignment_stats_test.sam OUTPUT=output_test_gc_nodict/test_nodic_ref_gc_summary_alignment_stats_test.txt CHART_OUTPUT=output_test_gc_nodict/test_nodic_ref_gc_summary_alignment_stats_test.pdf WINDOW_SIZE=100 MINIMUM_GENOME_FRACTION=1.0E-5 TMP_DIR=/tmp/raphael VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
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3 ## net.sf.picard.metrics.StringHeader
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4 # Started on: Tue Oct 26 13:54:53 EDT 2010
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5
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6 ## METRICS CLASS net.sf.picard.analysis.GcBiasDetailMetrics
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7 GC WINDOWS READ_STARTS MEAN_BASE_QUALITY NORMALIZED_COVERAGE ERROR_BAR_WIDTH
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8 6 3 0 0 0 0
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9 7 7 0 0 0 0
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10 8 6 0 0 0 0
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11 9 45 0 0 0 0
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12 10 54 0 0 0 0
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13 11 83 0 0 0 0
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14 12 110 0 0 0 0
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15 13 83 0 0 0 0
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16 14 130 0 0 0 0
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17 15 178 0 0 0 0
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18 16 276 0 0 0 0
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19 17 352 0 0 0 0
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20 18 519 0 0 0 0
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21 19 658 0 0 0 0
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22 20 1073 0 0 0 0
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23 21 1543 0 0 0 0
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24 22 2024 0 0 0 0
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25 23 2631 0 0 0 0
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26 24 3758 0 0 0 0
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27 25 5087 0 0 0 0
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28 26 6543 0 0 0 0
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29 27 8020 0 0 0 0
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30 28 10251 0 0 0 0
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31 29 12241 0 0 0 0
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32 30 14189 0 0 0 0
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33 31 16295 0 0 0 0
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34 32 17995 0 0 0 0
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35 33 20131 0 0 0 0
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36 34 22194 0 0 0 0
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37 35 23848 0 0 0 0
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38 36 25355 0 0 0 0
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39 37 27310 0 0 0 0
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40 38 28274 0 0 0 0
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41 39 28818 0 0 0 0
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42 40 28806 0 0 0 0
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43 41 29651 0 0 0 0
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44 42 30773 0 0 0 0
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45 43 31217 0 0 0 0
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46 44 31743 0 0 0 0
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47 45 32727 0 0 0 0
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48 46 34084 0 0 0 0
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49 47 35307 0 0 0 0
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50 48 36752 0 0 0 0
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51 49 36917 0 0 0 0
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52 50 36561 0 0 0 0
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53 51 36399 0 0 0 0
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54 52 35677 0 0 0 0
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55 53 34354 1 1 29.352448 29.352448
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56 54 32401 0 0 0 0
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57 55 30417 0 0 0 0
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58 56 28588 0 0 0 0
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59 57 27083 0 0 0 0
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60 58 24090 0 0 0 0
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61 59 20995 0 0 0 0
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62 60 17702 0 0 0 0
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63 61 14252 0 0 0 0
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64 62 11595 0 0 0 0
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65 63 9077 0 0 0 0
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66 64 6863 0 0 0 0
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67 65 5394 0 0 0 0
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68 66 4304 0 0 0 0
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69 67 3551 0 0 0 0
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70 68 2776 0 0 0 0
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71 69 2321 0 0 0 0
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72 70 1999 0 0 0 0
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73 71 1777 0 0 0 0
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74 72 1444 0 0 0 0
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75 73 1367 0 0 0 0
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76 74 1182 0 0 0 0
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77 75 975 0 0 0 0
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78 76 807 0 0 0 0
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79 77 852 0 0 0 0
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80 78 867 0 0 0 0
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81 79 925 0 0 0 0
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82 80 786 0 0 0 0
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83 81 762 0 0 0 0
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84 82 578 0 0 0 0
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85 83 475 0 0 0 0
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86 84 391 0 0 0 0
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87 85 219 0 0 0 0
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88 86 184 0 0 0 0
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89 87 75 0 0 0 0
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90 88 36 0 0 0 0
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91 89 37 0 0 0 0
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92 90 24 0 0 0 0
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93 91 40 0 0 0 0
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94 92 33 0 0 0 0
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95 93 11 0 0 0 0
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96 94 24 0 0 0 0
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97 95 12 0 0 0 0
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98 96 11 0 0 0 0
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99 97 11 0 0 0 0
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100 98 9 0 0 0 0
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101
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102
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