BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084380.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,951,435 number of mapped reads = 1,735,853 (58.81%) number of supplementary alignments = 9,625 (0.33%) number of secondary alignments = 0 number of mapped bases = 110,155,615 bp number of sequenced bases = 110,118,864 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 65,668 duplication rate = 3.14% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7664 >>>>>>> ACTG content number of A's = 30,708,357 bp (27.89%) number of C's = 20,880,791 bp (18.96%) number of T's = 33,794,346 bp (30.69%) number of G's = 24,734,094 bp (22.46%) number of N's = 1,276 bp (0%) GC percentage = 41.42% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 900,084 number of insertions = 8,070 mapped reads with insertion percentage = 0.46% number of deletions = 22,918 mapped reads with deletion percentage = 1.31% homopolymer indels = 46.72% >>>>>>> Coverage mean coverageData = 0.0356X std coverageData = 0.2804X There is a 3.11% of reference with a coverageData >= 1X There is a 0.34% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% 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 8939657 0.035866137320476325 0.4109782769827494 chr2 243199373 9700069 0.039885254967330856 0.35969683610154474 chr3 198022430 7833904 0.03956069017030041 0.2208038887846388 chr4 191154276 7474739 0.039103174443243946 0.22849025650970053 chr5 180915260 6066554 0.03353257210033029 0.20443489315651273 chr6 171115067 6722155 0.039284413218854654 0.2580625436157161 chr7 159138663 5616712 0.035294452612059456 0.3510711349996758 chr8 146364022 5751408 0.03929523062710042 0.281298759895784 chr9 141213431 4652845 0.03294902593224295 0.2767627464594524 chr10 135534747 5373774 0.03964868138205179 0.2881616748570176 chr11 135006516 4924426 0.036475469080322016 0.25837807376208427 chr12 133851895 5194088 0.038804740119667336 0.22225531863505432 chr13 115169878 3338933 0.028991373942412267 0.1898205696013869 chr14 107349540 3239128 0.030173655145611242 0.20141537280085306 chr15 102531392 2927259 0.028549880606322013 0.19283249836689847 chr16 90354753 3105748 0.03437282375172892 0.22048946882943618 chr17 81195210 2677655 0.03297799217466153 0.21781744623348873 chr18 78077248 2992890 0.038332421757488175 0.4877007829030199 chr19 59128983 2074257 0.035080207620009296 0.33719940664035647 chr20 63025520 2281250 0.03619565534723077 0.21849075701153153 chr21 48129895 1365965 0.028380801578727733 0.1964280774930326 chr22 51304566 1186330 0.023123283023191346 0.16828154063929573 chrMT 16571 55651 3.3583368535393157 2.62196309502306 chrX 155270560 6389336 0.04114969379900478 0.24298084489620447 chrY 59373566 270882 0.004562333345448714 0.10138666241787435