## htsjdk.samtools.metrics.StringHeader # picard.analysis.CollectGcBiasMetrics REFERENCE_SEQUENCE=/mnt/data/pipeline_genome_data/mm9/mm9.fa INPUT=/mnt/lab_data/kundaje/users/dskim89/ataqc/data/test_data/mouse/mouse_250kreads/align/rep1/mouse_250Kreads_rep1.1.trim.PE2SE.nodup.bam OUTPUT=/mnt/lab_data/kundaje/users/dskim89/ataqc/data/test_data/mouse/mouse_250kreads/qc/rep1/mouse_250Kreads_rep1.1.trim.PE2SE_gc.txt CHART_OUTPUT=/mnt/lab_data/kundaje/users/dskim89/ataqc/data/test_data/mouse/mouse_250kreads/qc/rep1/mouse_250Kreads_rep1.1.trim.PE2SE_gcPlot.pdf SUMMARY_OUTPUT=/mnt/lab_data/kundaje/users/dskim89/ataqc/data/test_data/mouse/mouse_250kreads/qc/rep1/mouse_250Kreads_rep1.1.trim.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: Fri Sep 22 12:22:30 PDT 2017 ## METRICS CLASS picard.analysis.GcBiasDetailMetrics GC WINDOWS READ_STARTS MEAN_BASE_QUALITY NORMALIZED_COVERAGE ERROR_BAR_WIDTH 0 5845 11 27 13.014096 3.923898 1 4258 0 0 0 0 2 5452 0 0 0 0 3 8525 0 0 0 0 4 14845 0 0 0 0 5 22053 0 0 0 0 6 36822 1 0 0.187801 0.187801 7 59686 4 0 0.46344 0.23172 8 88835 2 0 0.155687 0.110087 9 130396 5 0 0.265162 0.118584 10 187585 3 0 0.110593 0.063851 11 261036 11 20 0.291406 0.087862 12 365064 16 29 0.30308 0.07577 13 512158 19 30 0.25654 0.058854 14 719157 42 22 0.403861 0.062317 15 1020792 45 25 0.304846 0.045444 16 1469549 68 20 0.319986 0.038804 17 2117625 94 20 0.306962 0.031661 18 3024414 189 21 0.432142 0.031434 19 4281513 272 23 0.439316 0.026637 20 5969351 337 20 0.390399 0.021266 21 8148764 494 22 0.419219 0.018862 22 10877518 687 21 0.43675 0.016663 23 14204544 1029 22 0.500949 0.015617 24 18167394 1322 21 0.503205 0.01384 25 22716065 1607 21 0.489202 0.012203 26 27759085 2033 21 0.506452 0.011232 27 33299407 2465 21 0.511901 0.01031 28 39400132 3098 21 0.543738 0.009769 29 45996587 3685 21 0.55401 0.009126 30 52979848 4327 21 0.564784 0.008586 31 60367804 5183 21 0.59372 0.008247 32 68279272 5879 21 0.595416 0.007765 33 76483442 6547 21 0.591944 0.007316 34 83874763 7556 21 0.622969 0.007167 35 89997143 8061 21 0.619393 0.006899 36 95017893 8773 21 0.638482 0.006817 37 99519537 9439 21 0.655879 0.006751 38 102926845 10258 21 0.689191 0.006805 39 105213915 10688 21 0.702472 0.006795 40 106528827 11264 21 0.731192 0.006889 41 106663404 11829 21 0.766899 0.007051 42 106108223 12453 21 0.811579 0.007273 43 105536460 12995 21 0.85149 0.007469 44 104814734 13199 21 0.870812 0.00758 45 103439861 13720 21 0.917217 0.007831 46 101709820 14101 21 0.958722 0.008074 47 98578611 14262 21 1.000469 0.008377 48 94276268 14310 21 1.049647 0.008775 49 88247024 14011 21 1.097931 0.009276 50 81626880 13846 21 1.172997 0.009969 51 73669783 13147 21 1.234079 0.010763 52 65610340 12478 21 1.31516 0.011774 53 57307935 11671 21 1.408313 0.013036 54 49050914 10820 21 1.525408 0.014665 55 41336127 9685 21 1.620226 0.016464 56 34341725 8700 21 1.751874 0.018782 57 27979711 7630 21 1.885763 0.021589 58 22304596 6790 21 2.105141 0.025547 59 17335836 5744 21 2.291266 0.030232 60 13258043 5101 21 2.660613 0.037252 61 9970623 4519 21 3.134194 0.046623 62 7508885 3911 21 3.601788 0.057594 63 5706797 3418 20 4.141765 0.070843 64 4328604 3229 21 5.158531 0.09078 65 3318009 2939 21 6.125307 0.112987 66 2644993 2785 21 7.28126 0.137973 67 2097186 2632 21 8.678702 0.169166 68 1529745 2397 21 10.835647 0.22132 69 1219052 2269 22 12.871172 0.27021 70 1016540 2257 21 15.353696 0.323182 71 873995 2049 21 16.212084 0.358152 72 775645 1853 21 16.520313 0.383778 73 691903 1754 21 17.530335 0.418577 74 595230 1530 21 17.775117 0.45443 75 475107 1507 21 21.934496 0.565029 76 392275 1339 22 23.604553 0.645068 77 336877 1175 20 24.119725 0.703645 78 292153 1022 21 24.190586 0.756695 79 250930 947 21 26.09776 0.848063 80 216837 800 21 25.513054 0.902023 81 180589 659 21 25.234806 0.983008 82 145651 506 21 24.023866 1.067991 83 118895 426 21 24.777179 1.200458 84 90951 290 20 22.049379 1.294784 85 68684 236 21 23.760866 1.546701 86 50705 184 19 25.094172 1.849967 87 36328 124 22 23.604024 2.119704 88 24247 68 19 19.393524 2.35181 89 15058 46 22 21.124984 3.114709 90 8668 22 23 17.551313 3.741953 91 4967 6 20 8.353393 3.410259 92 2678 2 0 5.164464 3.651828 93 1507 4 23 18.354924 9.177462 94 934 0 0 0 0 95 386 0 0 0 0 96 157 0 0 0 0 97 85 0 0 0 0 98 10 0 0 0 0 99 15 0 0 0 0 100 28 0 0 0 0