BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818781.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,608,617 number of mapped reads = 1,518,673 (94.41%) number of supplementary alignments = 11,849 (0.74%) number of secondary alignments = 0 number of mapped bases = 103,008,295 bp number of sequenced bases = 102,964,842 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 762,202 duplication rate = 42.51% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.9207 >>>>>>> ACTG content number of A's = 29,825,520 bp (28.97%) number of C's = 21,992,016 bp (21.36%) number of T's = 29,787,054 bp (28.93%) number of G's = 21,353,892 bp (20.74%) number of N's = 6,360 bp (0.01%) GC percentage = 42.1% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 523,322 number of insertions = 13,551 mapped reads with insertion percentage = 0.88% number of deletions = 26,768 mapped reads with deletion percentage = 1.75% homopolymer indels = 39.81% >>>>>>> Coverage mean coverageData = 0.0333X std coverageData = 0.467X There is a 1.38% of reference with a coverageData >= 1X There is a 0.74% of reference with a coverageData >= 2X There is a 0.44% of reference with a coverageData >= 3X There is a 0.27% of reference with a coverageData >= 4X There is a 0.17% of reference with a coverageData >= 5X There is a 0.1% of reference with a coverageData >= 6X There is a 0.06% of reference with a coverageData >= 7X There is a 0.04% 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 0.01% of reference with a coverageData >= 11X There is a 0.01% 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 8195968 0.03288243763292369 0.5642639024110361 chr2 243199373 9347301 0.038434724911893585 0.7576279365419165 chr3 198022430 6856730 0.03462602696068319 0.36654848614544416 chr4 191154276 6797784 0.03556176791985548 0.4156096893038677 chr5 180915260 6447272 0.03563697169603051 0.384024993665044 chr6 171115067 5925245 0.03462725465315103 0.39685337706333285 chr7 159138663 5737475 0.03605330654311203 0.44625639873121664 chr8 146364022 5201825 0.03554032561362655 0.41187476403460516 chr9 141213431 4493922 0.03182361598451637 0.39394613515129895 chr10 135534747 5055035 0.03729696710172779 0.5219335784030955 chr11 135006516 4884254 0.03617791307198832 0.4034961011223463 chr12 133851895 4770853 0.03564277517326146 0.38413064883175607 chr13 115169878 3322199 0.028846075533743295 0.33843973079097794 chr14 107349540 3215175 0.029950524240718684 0.3746052990390556 chr15 102531392 2938702 0.028661485450231672 0.33577263754254505 chr16 90354753 3053322 0.03379259970972418 0.5305279731206233 chr17 81195210 2790513 0.03436795101582963 0.3872381575857015 chr18 78077248 2803944 0.03591243379889619 0.4675521500269119 chr19 59128983 1995070 0.033740982827321755 0.5200998079614289 chr20 63025520 2245768 0.03563267704891606 0.4016211077550584 chr21 48129895 1444595 0.03001450553756662 0.36272196402337364 chr22 51304566 1220278 0.02378497851438798 0.34449730094027936 chrMT 16571 175435 10.58686862591274 10.651343248611719 chrX 155270560 3219685 0.020735965658911774 0.29941615172512437 chrY 59373566 869945 0.014652059133520799 0.7684745448616565