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/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# 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## net.sf.picard.metrics.StringHeader
  4# Started on: Tue Oct 26 13:54:53 EDT 2010
  5
  6## METRICS CLASS	net.sf.picard.analysis.GcBiasDetailMetrics
  7GC	WINDOWS	READ_STARTS	MEAN_BASE_QUALITY	NORMALIZED_COVERAGE	ERROR_BAR_WIDTH
  86	3	0	0	0	0
  97	7	0	0	0	0
 108	6	0	0	0	0
 119	45	0	0	0	0
 1210	54	0	0	0	0
 1311	83	0	0	0	0
 1412	110	0	0	0	0
 1513	83	0	0	0	0
 1614	130	0	0	0	0
 1715	178	0	0	0	0
 1816	276	0	0	0	0
 1917	352	0	0	0	0
 2018	519	0	0	0	0
 2119	658	0	0	0	0
 2220	1073	0	0	0	0
 2321	1543	0	0	0	0
 2422	2024	0	0	0	0
 2523	2631	0	0	0	0
 2624	3758	0	0	0	0
 2725	5087	0	0	0	0
 2826	6543	0	0	0	0
 2927	8020	0	0	0	0
 3028	10251	0	0	0	0
 3129	12241	0	0	0	0
 3230	14189	0	0	0	0
 3331	16295	0	0	0	0
 3432	17995	0	0	0	0
 3533	20131	0	0	0	0
 3634	22194	0	0	0	0
 3735	23848	0	0	0	0
 3836	25355	0	0	0	0
 3937	27310	0	0	0	0
 4038	28274	0	0	0	0
 4139	28818	0	0	0	0
 4240	28806	0	0	0	0
 4341	29651	0	0	0	0
 4442	30773	0	0	0	0
 4543	31217	0	0	0	0
 4644	31743	0	0	0	0
 4745	32727	0	0	0	0
 4846	34084	0	0	0	0
 4947	35307	0	0	0	0
 5048	36752	0	0	0	0
 5149	36917	0	0	0	0
 5250	36561	0	0	0	0
 5351	36399	0	0	0	0
 5452	35677	0	0	0	0
 5553	34354	1	1	29.352448	29.352448
 5654	32401	0	0	0	0
 5755	30417	0	0	0	0
 5856	28588	0	0	0	0
 5957	27083	0	0	0	0
 6058	24090	0	0	0	0
 6159	20995	0	0	0	0
 6260	17702	0	0	0	0
 6361	14252	0	0	0	0
 6462	11595	0	0	0	0
 6563	9077	0	0	0	0
 6664	6863	0	0	0	0
 6765	5394	0	0	0	0
 6866	4304	0	0	0	0
 6967	3551	0	0	0	0
 7068	2776	0	0	0	0
 7169	2321	0	0	0	0
 7270	1999	0	0	0	0
 7371	1777	0	0	0	0
 7472	1444	0	0	0	0
 7573	1367	0	0	0	0
 7674	1182	0	0	0	0
 7775	975	0	0	0	0
 7876	807	0	0	0	0
 7977	852	0	0	0	0
 8078	867	0	0	0	0
 8179	925	0	0	0	0
 8280	786	0	0	0	0
 8381	762	0	0	0	0
 8482	578	0	0	0	0
 8583	475	0	0	0	0
 8684	391	0	0	0	0
 8785	219	0	0	0	0
 8886	184	0	0	0	0
 8987	75	0	0	0	0
 9088	36	0	0	0	0
 9189	37	0	0	0	0
 9290	24	0	0	0	0
 9391	40	0	0	0	0
 9492	33	0	0	0	0
 9593	11	0	0	0	0
 9694	24	0	0	0	0
 9795	12	0	0	0	0
 9896	11	0	0	0	0
 9997	11	0	0	0	0
10098	9	0	0	0	0
101
102