BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234048.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 = 4,372,673 number of mapped reads = 4,086,495 (93.46%) number of supplementary alignments = 23,095 (0.53%) number of secondary alignments = 0 number of mapped bases = 257,203,826 bp number of sequenced bases = 257,098,910 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 375,732 duplication rate = 7.25% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.8985 >>>>>>> ACTG content number of A's = 64,260,308 bp (24.99%) number of C's = 46,793,550 bp (18.2%) number of T's = 83,811,130 bp (32.6%) number of G's = 62,209,952 bp (24.2%) number of N's = 23,970 bp (0.01%) GC percentage = 42.4% >>>>>>> Mismatches and indels general error rate = 0.0061 number of mismatches = 1,546,078 number of insertions = 17,370 mapped reads with insertion percentage = 0.42% number of deletions = 59,936 mapped reads with deletion percentage = 1.45% homopolymer indels = 42.95% >>>>>>> Coverage mean coverageData = 0.0831X std coverageData = 0.9616X There is a 6.57% of reference with a coverageData >= 1X There is a 1.17% of reference with a coverageData >= 2X There is a 0.25% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% 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% 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 22716636 0.0911397368193518 2.1454684528990824 chr2 243199373 16942544 0.06966524539518447 1.5280176667409693 chr3 198022430 25061524 0.12655901657201157 0.43818742012294065 chr4 191154276 9172032 0.04798235326946074 0.33618000880675875 chr5 180915260 13986841 0.07731156011936197 0.3524297751940407 chr6 171115067 15599794 0.09116551963247047 0.6443200910487078 chr7 159138663 18131772 0.1139369381279771 1.4524544247533275 chr8 146364022 11541788 0.0788567288756249 0.6969154194047997 chr9 141213431 12396088 0.08778264158173453 0.628004609491414 chr10 135534747 11762425 0.08678530974791283 0.7779663108187477 chr11 135006516 11784195 0.08728612032325907 0.5714925342614368 chr12 133851895 7983200 0.05964203943470505 0.32755736135884916 chr13 115169878 12261142 0.1064613613639497 0.4573545644548969 chr14 107349540 10411691 0.09698868760872194 0.4473132431296324 chr15 102531392 5444538 0.05310118095343912 0.3583199643169579 chr16 90354753 8263908 0.0914606894005897 0.4676198601173909 chr17 81195210 6593109 0.08120071368742073 0.4038889991679254 chr18 78077248 5481931 0.0702116319468637 1.4218536401994852 chr19 59128983 7936275 0.13421971083115028 1.1994799515999155 chr20 63025520 7659278 0.12152661334646664 0.47675464873425305 chr21 48129895 4842542 0.10061401546793318 0.42216012265366243 chr22 51304566 2158222 0.04206686009194581 0.2452681931760817 chrMT 16571 91661 5.531410295093838 3.6769505293430376 chrX 155270560 8313013 0.05353888721725483 0.39073463861376434 chrY 59373566 667677 0.011245357908938804 0.2637563716193572