BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013240.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 = 1,810,671 number of mapped reads = 1,596,066 (88.15%) number of supplementary alignments = 20,500 (1.13%) number of secondary alignments = 0 number of mapped bases = 104,995,140 bp number of sequenced bases = 104,947,493 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 96,845 duplication rate = 5.16% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.7817 >>>>>>> ACTG content number of A's = 28,697,333 bp (27.34%) number of C's = 19,735,680 bp (18.81%) number of T's = 32,837,588 bp (31.29%) number of G's = 23,650,556 bp (22.54%) number of N's = 26,336 bp (0.03%) GC percentage = 41.34% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 821,438 number of insertions = 7,097 mapped reads with insertion percentage = 0.44% number of deletions = 27,342 mapped reads with deletion percentage = 1.69% homopolymer indels = 45.69% >>>>>>> Coverage mean coverageData = 0.0339X std coverageData = 0.2731X There is a 2.54% of reference with a coverageData >= 1X There is a 0.6% of reference with a coverageData >= 2X There is a 0.15% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% 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 12173425 0.04884009897812852 0.31243934625984626 chr2 243199373 8649528 0.035565585113576756 0.3179205118228261 chr3 198022430 8555190 0.04320313612957886 0.2651597225487018 chr4 191154276 3699110 0.01935143736988651 0.1861192585288083 chr5 180915260 2837192 0.015682436075320567 0.16021927724434862 chr6 171115067 7429310 0.043417041703288466 0.2856180310938659 chr7 159138663 4961864 0.03117950035812479 0.2567990652821314 chr8 146364022 5048657 0.03449383892989768 0.2976998762332281 chr9 141213431 4045442 0.02864771411155643 0.24804783703481834 chr10 135534747 5343732 0.03942702604521038 0.3036025689852339 chr11 135006516 8488121 0.06287193575160475 0.404387585197152 chr12 133851895 2612391 0.019517026636044262 0.17723245468990498 chr13 115169878 1766201 0.015335615793567134 0.15694057221310237 chr14 107349540 940075 0.008757140459102107 0.12330251311439716 chr15 102531392 6015870 0.05867344510450029 0.3131891123888946 chr16 90354753 6307893 0.0698125199899556 0.38122164732559116 chr17 81195210 1121675 0.013814546449230195 0.16950672178188597 chr18 78077248 1361746 0.017441009191307564 0.41453476417045915 chr19 59128983 992851 0.016791274762835005 0.248147095483905 chr20 63025520 552412 0.008764893966761401 0.12038915642383644 chr21 48129895 1597443 0.03319024485717245 0.2424805404998064 chr22 51304566 1537177 0.029961797162459187 0.2204784977396631 chrMT 16571 8518 0.5140305352724639 0.957789105837336 chrX 155270560 8628726 0.055572196042830015 0.32951533897043295 chrY 59373566 320591 0.005399557776266967 0.120297070835255