BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008816.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,671,411 number of mapped reads = 1,300,912 (77.83%) number of supplementary alignments = 6,143 (0.37%) number of secondary alignments = 0 number of mapped bases = 80,876,913 bp number of sequenced bases = 80,826,891 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 43,736 duplication rate = 2.56% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8738 >>>>>>> ACTG content number of A's = 23,226,335 bp (28.74%) number of C's = 14,812,214 bp (18.33%) number of T's = 23,884,882 bp (29.55%) number of G's = 18,889,992 bp (23.37%) number of N's = 13,468 bp (0.02%) GC percentage = 41.7% >>>>>>> Mismatches and indels general error rate = 0.0095 number of mismatches = 759,922 number of insertions = 6,684 mapped reads with insertion percentage = 0.51% number of deletions = 31,718 mapped reads with deletion percentage = 2.41% homopolymer indels = 48.09% >>>>>>> Coverage mean coverageData = 0.0261X std coverageData = 0.2345X There is a 2.28% of reference with a coverageData >= 1X There is a 0.23% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 6943883 0.02785903991789854 0.30559185795221083 chr2 243199373 7572307 0.03113621102962301 0.3010681781988563 chr3 198022430 5881444 0.029700898024531866 0.19694761420805815 chr4 191154276 4102546 0.021461963006257835 0.1700380887691485 chr5 180915260 4003216 0.02212757508681136 0.16727315911657276 chr6 171115067 4058331 0.023716970522531484 0.195168576493392 chr7 159138663 4394690 0.027615476447731623 0.33208079706870414 chr8 146364022 5736384 0.039192582450351086 0.25798128774677415 chr9 141213431 2579775 0.01826862347109178 0.21856455226245797 chr10 135534747 3921354 0.028932462610492052 0.24253145391091638 chr11 135006516 3328666 0.024655595141793007 0.261418701848483 chr12 133851895 3495773 0.02611672401051924 0.18455233193167903 chr13 115169878 2337089 0.020292536907957827 0.16455183127902206 chr14 107349540 2985986 0.027815545367031846 0.1932699541553067 chr15 102531392 2040304 0.01989931044728233 0.16127250755538125 chr16 90354753 2003842 0.02217749408268539 0.179777350111785 chr17 81195210 2087499 0.025709632378560263 0.2208473646229201 chr18 78077248 1454584 0.018630062371050783 0.355857460910829 chr19 59128983 1366476 0.02311008799187363 0.2211984841338113 chr20 63025520 1725586 0.027379163234194655 0.18909782035507003 chr21 48129895 826755 0.01717757747030198 0.1546952636920828 chr22 51304566 863768 0.01683608433604136 0.14598829087310589 chrMT 16571 27606 1.6659223945446866 1.7632118407916206 chrX 155270560 6886189 0.044349611413779924 0.24917620705605203 chrY 59373566 252860 0.004258797593528406 0.08737960960082898