BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714240.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 = 192,120 number of mapped reads = 132,927 (69.19%) number of supplementary alignments = 4,900 (2.55%) number of secondary alignments = 0 number of mapped bases = 16,997,576 bp number of sequenced bases = 16,679,134 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 101,711 duplication rate = 40.97% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 51.4014 >>>>>>> ACTG content number of A's = 4,732,358 bp (28.37%) number of C's = 3,467,547 bp (20.79%) number of T's = 4,460,707 bp (26.74%) number of G's = 4,018,397 bp (24.09%) number of N's = 125 bp (0%) GC percentage = 44.88% >>>>>>> Mismatches and indels general error rate = 0.0421 number of mismatches = 638,172 number of insertions = 19,385 mapped reads with insertion percentage = 14.06% number of deletions = 54,586 mapped reads with deletion percentage = 39.09% homopolymer indels = 28.94% >>>>>>> Coverage mean coverageData = 0.0055X std coverageData = 0.7947X There is a 0.03% of reference with a coverageData >= 1X There is a 0.02% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% 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 1475149 0.005918336307775939 0.6890876947483313 chr2 243199373 1807660 0.00743283166276913 1.783742766690612 chr3 198022430 880873 0.004448349613728101 0.5144854947131592 chr4 191154276 844917 0.0044200789942046605 0.6119715914037355 chr5 180915260 888789 0.004912736493317369 0.5692087813130832 chr6 171115067 728439 0.004257012621804952 0.49322357030455666 chr7 159138663 765210 0.0048084480890731125 0.547585715381568 chr8 146364022 796490 0.005441842804784361 0.7316011374945041 chr9 141213431 678966 0.004808083729655998 0.6935974085344337 chr10 135534747 834910 0.006160117744566269 0.575061735199962 chr11 135006516 884821 0.006553913294081302 0.6814952733191861 chr12 133851895 743255 0.005552816416980873 0.7436489800630817 chr13 115169878 526870 0.004574720483770939 0.5840170016308212 chr14 107349540 576830 0.00537338119939778 0.6326716274431519 chr15 102531392 465779 0.0045427940742285055 0.4746428634698702 chr16 90354753 476782 0.005276778300749713 0.542445231824448 chr17 81195210 615937 0.007585878526578107 1.0262529454641756 chr18 78077248 432215 0.005535735583303346 0.5633174692688747 chr19 59128983 286819 0.004850734537409513 0.6285120547923712 chr20 63025520 349551 0.005546181927574735 0.5383134905348362 chr21 48129895 160179 0.003328056294326011 0.3869086887157388 chr22 51304566 164900 0.003214138874111127 0.39371235217711653 chrMT 16571 138269 8.344034759519642 74.89458078131608 chrX 155270560 1403102 0.009036497324412304 0.6491301697794218 chrY 59373566 70864 0.0011935277729486554 0.28217400150086963