/test-data/picard_output_gc_summary_alignment_stats.txt

https://bitbucket.org/cistrome/cistrome-harvard/ · Plain Text · 102 lines · 99 code · 3 blank · 0 comment · 0 complexity · 57e06fe9562117fd89fb21bccb493be8 MD5 · raw file 

    

  1. ## net.sf.picard.metrics.StringHeader
    2. 

  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
    3. 

  3. ## net.sf.picard.metrics.StringHeader
    4. 

  4. # Started on: Tue Oct 26 13:54:53 EDT 2010
    5. 

  5. 

  6. ## METRICS CLASS	net.sf.picard.analysis.GcBiasDetailMetrics
    7. 

  7. GC	WINDOWS	READ_STARTS	MEAN_BASE_QUALITY	NORMALIZED_COVERAGE	ERROR_BAR_WIDTH
    8. 

  8. 6	3	0	0	0	0
    9. 

  9. 7	7	0	0	0	0
    10. 

  10. 8	6	0	0	0	0
    11. 

  11. 9	45	0	0	0	0
    12. 

  12. 10	54	0	0	0	0
    13. 

  13. 11	83	0	0	0	0
    14. 

  14. 12	110	0	0	0	0
    15. 

  15. 13	83	0	0	0	0
    16. 

  16. 14	130	0	0	0	0
    17. 

  17. 15	178	0	0	0	0
    18. 

  18. 16	276	0	0	0	0
    19. 

  19. 17	352	0	0	0	0
    20. 

  20. 18	519	0	0	0	0
    21. 

  21. 19	658	0	0	0	0
    22. 

  22. 20	1073	0	0	0	0
    23. 

  23. 21	1543	0	0	0	0
    24. 

  24. 22	2024	0	0	0	0
    25. 

  25. 23	2631	0	0	0	0
    26. 

  26. 24	3758	0	0	0	0
    27. 

  27. 25	5087	0	0	0	0
    28. 

  28. 26	6543	0	0	0	0
    29. 

  29. 27	8020	0	0	0	0
    30. 

  30. 28	10251	0	0	0	0
    31. 

  31. 29	12241	0	0	0	0
    32. 

  32. 30	14189	0	0	0	0
    33. 

  33. 31	16295	0	0	0	0
    34. 

  34. 32	17995	0	0	0	0
    35. 

  35. 33	20131	0	0	0	0
    36. 

  36. 34	22194	0	0	0	0
    37. 

  37. 35	23848	0	0	0	0
    38. 

  38. 36	25355	0	0	0	0
    39. 

  39. 37	27310	0	0	0	0
    40. 

  40. 38	28274	0	0	0	0
    41. 

  41. 39	28818	0	0	0	0
    42. 

  42. 40	28806	0	0	0	0
    43. 

  43. 41	29651	0	0	0	0
    44. 

  44. 42	30773	0	0	0	0
    45. 

  45. 43	31217	0	0	0	0
    46. 

  46. 44	31743	0	0	0	0
    47. 

  47. 45	32727	0	0	0	0
    48. 

  48. 46	34084	0	0	0	0
    49. 

  49. 47	35307	0	0	0	0
    50. 

  50. 48	36752	0	0	0	0
    51. 

  51. 49	36917	0	0	0	0
    52. 

  52. 50	36561	0	0	0	0
    53. 

  53. 51	36399	0	0	0	0
    54. 

  54. 52	35677	0	0	0	0
    55. 

  55. 53	34354	1	1	29.352448	29.352448
    56. 

  56. 54	32401	0	0	0	0
    57. 

  57. 55	30417	0	0	0	0
    58. 

  58. 56	28588	0	0	0	0
    59. 

  59. 57	27083	0	0	0	0
    60. 

  60. 58	24090	0	0	0	0
    61. 

  61. 59	20995	0	0	0	0
    62. 

  62. 60	17702	0	0	0	0
    63. 

  63. 61	14252	0	0	0	0
    64. 

  64. 62	11595	0	0	0	0
    65. 

  65. 63	9077	0	0	0	0
    66. 

  66. 64	6863	0	0	0	0
    67. 

  67. 65	5394	0	0	0	0
    68. 

  68. 66	4304	0	0	0	0
    69. 

  69. 67	3551	0	0	0	0
    70. 

  70. 68	2776	0	0	0	0
    71. 

  71. 69	2321	0	0	0	0
    72. 

  72. 70	1999	0	0	0	0
    73. 

  73. 71	1777	0	0	0	0
    74. 

  74. 72	1444	0	0	0	0
    75. 

  75. 73	1367	0	0	0	0
    76. 

  76. 74	1182	0	0	0	0
    77. 

  77. 75	975	0	0	0	0
    78. 

  78. 76	807	0	0	0	0
    79. 

  79. 77	852	0	0	0	0
    80. 

  80. 78	867	0	0	0	0
    81. 

  81. 79	925	0	0	0	0
    82. 

  82. 80	786	0	0	0	0
    83. 

  83. 81	762	0	0	0	0
    84. 

  84. 82	578	0	0	0	0
    85. 

  85. 83	475	0	0	0	0
    86. 

  86. 84	391	0	0	0	0
    87. 

  87. 85	219	0	0	0	0
    88. 

  88. 86	184	0	0	0	0
    89. 

  89. 87	75	0	0	0	0
    90. 

  90. 88	36	0	0	0	0
    91. 

  91. 89	37	0	0	0	0
    92. 

  92. 90	24	0	0	0	0
    93. 

  93. 91	40	0	0	0	0
    94. 

  94. 92	33	0	0	0	0
    95. 

  95. 93	11	0	0	0	0
    96. 

  96. 94	24	0	0	0	0
    97. 

  97. 95	12	0	0	0	0
    98. 

  98. 96	11	0	0	0	0
    99. 

  99. 97	11	0	0	0	0
    100. 

  100. 98	9	0	0	0	0
    101.