## htsjdk.samtools.metrics.StringHeader # picard.analysis.CollectGcBiasMetrics REFERENCE_SEQUENCE=/mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/encodeHg19Male.fa INPUT=/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.bam OUTPUT=/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/qc/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.PE2SE_gc.txt CHART_OUTPUT=/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/qc/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.PE2SE_gcPlot.pdf SUMMARY_OUTPUT=/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/qc/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.PE2SE_gcSummary.txt ASSUME_SORTED=false VERBOSITY=ERROR QUIET=true WINDOW_SIZE=100 MINIMUM_GENOME_FRACTION=1.0E-5 IS_BISULFITE_SEQUENCED=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false ## htsjdk.samtools.metrics.StringHeader # Started on: Wed Jun 22 18:25:38 PDT 2016 ## METRICS CLASS picard.analysis.GcBiasDetailMetrics GC WINDOWS READ_STARTS MEAN_BASE_QUALITY NORMALIZED_COVERAGE ERROR_BAR_WIDTH 0 132617 1096 14 0.897138 0.027099 1 94890 0 0 0 0 2 109162 3 20 0.002983 0.001722 3 138935 2 18 0.001563 0.001105 4 149105 10 14 0.00728 0.002302 5 152159 9 17 0.006421 0.00214 6 173090 24 20 0.015052 0.003072 7 186762 37 21 0.021506 0.003536 8 213164 39 19 0.019861 0.00318 9 241390 73 19 0.032829 0.003842 10 285622 131 18 0.049788 0.00435 11 350736 203 20 0.06283 0.00441 12 459629 349 21 0.082426 0.004412 13 608567 598 21 0.10667 0.004362 14 864796 1108 21 0.139083 0.004178 15 1274785 1916 22 0.163157 0.003727 16 1909046 3339 22 0.189866 0.003286 17 2868490 5748 23 0.217526 0.002869 18 4303763 9623 22 0.242723 0.002474 19 6353569 14972 22 0.255806 0.002091 20 9179194 23511 22 0.278045 0.001813 21 12913078 35415 23 0.297718 0.001582 22 17634823 50785 23 0.312617 0.001387 23 23411495 69953 23 0.324358 0.001226 24 30221753 95023 23 0.341316 0.001107 25 37904212 125297 23 0.35884 0.001014 26 46166684 159388 23 0.374779 0.000939 27 54796353 196372 23 0.389024 0.000878 28 63501084 237898 23 0.406685 0.000834 29 71973467 283321 23 0.427321 0.000803 30 80017898 328183 23 0.445222 0.000777 31 87437255 373202 23 0.463335 0.000758 32 93940211 419290 23 0.484519 0.000748 33 99388467 463005 23 0.505706 0.000743 34 103623497 505450 23 0.529502 0.000745 35 106826768 546918 23 0.555764 0.000752 36 108862831 582812 23 0.581162 0.000761 37 109522683 614041 23 0.608613 0.000777 38 108510517 641432 23 0.641692 0.000801 39 106131033 662949 23 0.678088 0.000833 40 102776654 679503 23 0.717703 0.000871 41 98739995 697017 23 0.766299 0.000918 42 94248164 722562 23 0.832243 0.000979 43 89762722 731521 23 0.884665 0.001034 44 85709976 730759 24 0.925531 0.001083 45 82258561 734383 24 0.969147 0.001131 46 79354635 726150 24 0.99335 0.001166 47 76895966 726244 24 1.025244 0.001203 48 74317641 717176 24 1.047567 0.001237 49 71107038 700142 24 1.068862 0.001277 50 67012148 682701 24 1.105923 0.001338 51 62221585 660843 24 1.152936 0.001418 52 57246507 632104 24 1.198637 0.001508 53 52587634 617912 24 1.275531 0.001623 54 48433939 600099 24 1.344996 0.001736 55 44773565 584152 25 1.41629 0.001853 56 41250459 565879 24 1.489165 0.00198 57 37506100 553539 24 1.602117 0.002153 58 33378999 532897 24 1.733078 0.002374 59 28901341 514028 24 1.930709 0.002693 60 24406896 492101 24 2.188718 0.00312 61 20260501 472045 24 2.529189 0.003681 62 16721383 451317 24 2.929932 0.004361 63 13801920 432948 24 3.405213 0.005175 64 11394997 415460 24 3.957884 0.00614 65 9391555 396474 24 4.58274 0.007278 66 7732362 379508 24 5.327909 0.008649 67 6279229 359567 23 6.216151 0.010366 68 5020138 341876 23 7.392665 0.012643 69 4016215 324907 23 8.781934 0.015407 70 3221098 306211 23 10.319648 0.018649 71 2580218 284450 22 11.967339 0.022439 72 2088005 265769 22 13.817225 0.026802 73 1704477 248606 22 15.833193 0.031755 74 1405875 232264 22 17.934251 0.037213 75 1185140 213914 21 19.593751 0.042364 76 1023619 194357 21 20.611514 0.046753 77 899940 173608 21 20.941328 0.05026 78 800553 154468 20 20.945777 0.053294 79 698967 134233 20 20.847341 0.056901 80 596517 114371 20 20.813309 0.061544 81 501530 94617 20 20.479545 0.066579 82 420889 77579 19 20.008966 0.071838 83 346018 61615 19 19.330176 0.077874 84 268266 46061 19 18.638706 0.086846 85 194343 34069 18 19.029988 0.1031 86 129239 23965 18 20.129449 0.13003 87 83780 16499 17 21.377913 0.166432 88 57779 10941 17 20.555831 0.19652 89 37497 7402 16 21.428935 0.249073 90 24583 4366 16 19.27955 0.29178 91 15587 2453 15 17.083744 0.344933 92 9206 1280 15 15.093398 0.421873 93 5777 788 15 14.807164 0.527483 94 3352 362 14 11.723373 0.616167 95 1653 116 14 7.617863 0.707301 96 986 36 12 3.963452 0.660575 97 658 5 10 0.824883 0.368899 98 328 6 10 1.985754 0.810681 99 133 3 8 2.448599 1.413699 100 339 0 0 0 0