BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472691.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 15,619,410 number of mapped reads = 15,474,682 (99.07%) number of supplementary alignments = 110,865 (0.71%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,757,037 number of mapped paired reads (second in pair) = 7,717,645 number of mapped paired reads (both in pair) = 15,376,744 number of mapped paired reads (singletons) = 97,938 number of mapped bases = 1,523,185,206 bp number of sequenced bases = 1,523,018,430 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,238,651 duplication rate = 47.8% >>>>>>> Insert size mean insert size = 28,678.2442 std insert size = 1,667,699.8627 median insert size = 217 >>>>>>> Mapping quality mean mapping quality = 54.504 >>>>>>> ACTG content number of A's = 415,735,228 bp (27.3%) number of C's = 347,645,417 bp (22.83%) number of T's = 416,802,223 bp (27.37%) number of G's = 342,549,200 bp (22.49%) number of N's = 286,362 bp (0.02%) GC percentage = 45.32% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 9,545,740 number of insertions = 93,850 mapped reads with insertion percentage = 0.6% number of deletions = 71,639 mapped reads with deletion percentage = 0.45% homopolymer indels = 47.62% >>>>>>> Coverage mean coverageData = 0.492X std coverageData = 32.4551X There is a 3.16% of reference with a coverageData >= 1X There is a 1.52% of reference with a coverageData >= 2X There is a 0.76% of reference with a coverageData >= 3X There is a 0.55% of reference with a coverageData >= 4X There is a 0.41% of reference with a coverageData >= 5X There is a 0.35% of reference with a coverageData >= 6X There is a 0.3% of reference with a coverageData >= 7X There is a 0.28% of reference with a coverageData >= 8X There is a 0.26% of reference with a coverageData >= 9X There is a 0.24% of reference with a coverageData >= 10X There is a 0.23% of reference with a coverageData >= 11X There is a 0.22% of reference with a coverageData >= 12X There is a 0.21% of reference with a coverageData >= 13X There is a 0.21% of reference with a coverageData >= 14X There is a 0.2% of reference with a coverageData >= 15X There is a 0.19% of reference with a coverageData >= 16X There is a 0.19% of reference with a coverageData >= 17X There is a 0.18% of reference with a coverageData >= 18X There is a 0.18% of reference with a coverageData >= 19X There is a 0.17% of reference with a coverageData >= 20X There is a 0.17% of reference with a coverageData >= 21X There is a 0.17% of reference with a coverageData >= 22X There is a 0.16% of reference with a coverageData >= 23X There is a 0.16% of reference with a coverageData >= 24X There is a 0.16% of reference with a coverageData >= 25X There is a 0.15% of reference with a coverageData >= 26X There is a 0.15% of reference with a coverageData >= 27X There is a 0.15% of reference with a coverageData >= 28X There is a 0.14% of reference with a coverageData >= 29X There is a 0.14% of reference with a coverageData >= 30X There is a 0.14% of reference with a coverageData >= 31X There is a 0.14% of reference with a coverageData >= 32X There is a 0.13% of reference with a coverageData >= 33X There is a 0.13% of reference with a coverageData >= 34X There is a 0.13% of reference with a coverageData >= 35X There is a 0.13% of reference with a coverageData >= 36X There is a 0.13% of reference with a coverageData >= 37X There is a 0.13% of reference with a coverageData >= 38X There is a 0.12% of reference with a coverageData >= 39X There is a 0.12% of reference with a coverageData >= 40X There is a 0.12% of reference with a coverageData >= 41X There is a 0.12% of reference with a coverageData >= 42X There is a 0.12% of reference with a coverageData >= 43X There is a 0.12% of reference with a coverageData >= 44X There is a 0.11% of reference with a coverageData >= 45X There is a 0.11% of reference with a coverageData >= 46X There is a 0.11% of reference with a coverageData >= 47X There is a 0.11% of reference with a coverageData >= 48X There is a 0.11% of reference with a coverageData >= 49X There is a 0.11% of reference with a coverageData >= 50X There is a 0.11% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 226028783 0.9068333795645789 49.747470312348476 chr2 243199373 87589712 0.3601559943166465 32.95974874517418 chr3 198022430 139595858 0.704949727159696 33.309399099194266 chr4 191154276 46053095 0.2409210819851082 12.461637752969377 chr5 180915260 74593042 0.4123092877847894 22.237197377269542 chr6 171115067 126851769 0.7413243685899383 32.146588521764755 chr7 159138663 81313064 0.5109573152565696 29.2829427764878 chr8 146364022 61502645 0.420203299687952 18.47829864602434 chr9 141213431 43322076 0.3067843879524462 12.957354560971762 chr10 135534747 27488136 0.2028124640244468 11.173903972145695 chr11 135006516 76831605 0.5690955316556721 45.91048384367152 chr12 133851895 95463717 0.7132040752953105 62.61930657170484 chr13 115169878 42218802 0.3665785076198483 21.354894719649494 chr14 107349540 28752773 0.2678425357015969 10.02702326707556 chr15 102531392 30854661 0.3009289194084091 16.09110139710476 chr16 90354753 103305909 1.1433367428938686 76.1158693449564 chr17 81195210 62321599 0.7675526548918341 26.21861541670645 chr18 78077248 12666236 0.16222697808201436 7.507546688429864 chr19 59128983 46828879 0.7919784279056516 37.42998405033509 chr20 63025520 16955926 0.2690327029431887 9.56429786315257 chr21 48129895 11883114 0.24689673642545865 15.497814403629976 chr22 51304566 17636240 0.3437557585030541 14.383673714844873 chrMT 16571 3016 0.18200470701828494 0.5259010850131062 chrX 155270560 60254988 0.38806447275001776 16.07552285101452 chrY 59373566 2869561 0.048330615681732844 7.005622173020616