BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714050.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 413,978 number of mapped reads = 99,635 (24.07%) number of supplementary alignments = 3,335 (0.81%) number of secondary alignments = 0 number of mapped bases = 10,462,857 bp number of sequenced bases = 10,350,448 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 91,308 duplication rate = 29.61% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 27.4652 >>>>>>> ACTG content number of A's = 1,897,326 bp (18.33%) number of C's = 1,274,124 bp (12.31%) number of T's = 1,592,297 bp (15.38%) number of G's = 5,586,367 bp (53.97%) number of N's = 334 bp (0%) GC percentage = 66.28% >>>>>>> Mismatches and indels general error rate = 0.0342 number of mismatches = 305,447 number of insertions = 9,539 mapped reads with insertion percentage = 7.85% number of deletions = 20,562 mapped reads with deletion percentage = 19.57% homopolymer indels = 29.22% >>>>>>> Coverage mean coverageData = 0.0034X std coverageData = 6.0135X There is a 0.01% of reference with a coverageData >= 1X There is a 0.01% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 147676 5.924799681843119E-4 0.1546080241195913 chr2 243199373 4930320 0.020272749634103703 19.97070483960102 chr3 198022430 2312915 0.011680065738007558 8.31441112567132 chr4 191154276 173700 9.086901095531863E-4 0.2785199387867721 chr5 180915260 123748 6.840108457407076E-4 0.17983925269156065 chr6 171115067 336359 0.001965688971152961 1.0169959012016665 chr7 159138663 77274 4.855765314554641E-4 0.1818104450412203 chr8 146364022 110975 7.582122879897357E-4 0.1773597430915616 chr9 141213431 488687 0.003460626914446969 1.7746944264541238 chr10 135534747 49435 3.6474041597613343E-4 0.07318805914729895 chr11 135006516 239030 0.0017705071361148227 0.8666118536060788 chr12 133851895 335454 0.002506158018905896 1.5864580075591206 chr13 115169878 27343 2.374145086790836E-4 0.04466015751408399 chr14 107349540 85773 7.99006684146015E-4 0.17876898880032593 chr15 102531392 142440 0.0013892330653230574 0.5709322124127844 chr16 90354753 88924 9.84165160630786E-4 0.28759049797390157 chr17 81195210 31510 3.880770799164138E-4 0.12430065249992799 chr18 78077248 48234 6.177727985494571E-4 0.22128265706437422 chr19 59128983 46348 7.838457157296279E-4 0.2001329150946447 chr20 63025520 65666 0.001041895409986304 0.2863908229725638 chr21 48129895 13230 2.7488113157113684E-4 0.06659589527184728 chr22 51304566 6223 1.2129524689868734E-4 0.024420584651541514 chrMT 16571 172650 10.418803934584515 74.8526277051829 chrX 155270560 401749 0.0025874125784050754 0.29302776551635945 chrY 59373566 7194 1.21165031589984E-4 0.030507973644860832