BamQC report ----------------------------------- >>>>>>> Input bam file = SRR620539.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP016866/SRP016866.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 = 11,747,486 number of mapped reads = 5,945,531 (50.61%) number of supplementary alignments = 176 (0%) number of secondary alignments = 0 number of mapped bases = 260,564,549 bp number of sequenced bases = 260,488,282 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 622,242 duplication rate = 5.65% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.6008 >>>>>>> ACTG content number of A's = 67,150,358 bp (25.78%) number of C's = 47,201,485 bp (18.12%) number of T's = 80,464,563 bp (30.89%) number of G's = 65,668,555 bp (25.21%) number of N's = 3,321 bp (0%) GC percentage = 43.33% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 1,998,045 number of insertions = 21,850 mapped reads with insertion percentage = 0.37% number of deletions = 53,472 mapped reads with deletion percentage = 0.87% homopolymer indels = 39.71% >>>>>>> Coverage mean coverageData = 0.0842X std coverageData = 0.9681X There is a 6.46% of reference with a coverageData >= 1X There is a 0.95% of reference with a coverageData >= 2X There is a 0.27% of reference with a coverageData >= 3X There is a 0.13% of reference with a coverageData >= 4X There is a 0.08% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% 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% 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 20967795 0.08412334106080321 1.4928109160940495 chr2 243199373 23105539 0.09500657306382118 0.9928280996742745 chr3 198022430 16953160 0.08561232179607128 0.8346604854080388 chr4 191154276 17389704 0.09097208999917951 0.7537571596193148 chr5 180915260 15276898 0.08444228529975857 0.4367435313326073 chr6 171115067 14793539 0.08645374869297746 0.6125632808844319 chr7 159138663 15091458 0.0948321276269614 1.140038959634501 chr8 146364022 12911843 0.08821732843608247 0.7288060330047044 chr9 141213431 10920888 0.07733604319832722 0.6898358766610594 chr10 135534747 13877753 0.1023925842426223 2.2429222627007865 chr11 135006516 12073332 0.08942777250840249 0.8978169482799583 chr12 133851895 12061042 0.09010736829687768 0.48015989488723715 chr13 115169878 7318227 0.06354289096320828 0.4058266049559086 chr14 107349540 7552898 0.0703579912871541 0.4722807344678684 chr15 102531392 7468910 0.07284510484359756 0.3932468142394633 chr16 90354753 8108916 0.0897453175484858 0.6443416616672434 chr17 81195210 7556915 0.0930709459338796 0.5984760825176412 chr18 78077248 6570185 0.08414980251353121 1.8125652432405608 chr19 59128983 6108556 0.10330899822849988 1.0590528708052178 chr20 63025520 5568624 0.08835506632868717 0.5993512577305815 chr21 48129895 3382783 0.070284445872986 0.576347095361976 chr22 51304566 3320929 0.06472969676812002 0.4126660750940547 chrMT 16571 93217 5.625309275239877 5.283720867401305 chrX 155270560 8972547 0.05778653081434111 0.6032483355273148 chrY 59373566 3118891 0.052529959207772696 0.7612775676041978