BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5514729.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP106579/SRP106579.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 = 106,655,060 number of mapped reads = 100,024,744 (93.78%) number of supplementary alignments = 3,129,348 (2.93%) number of secondary alignments = 0 number of mapped bases = 9,421,086,028 bp number of sequenced bases = 9,414,669,976 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 82,659,332 duplication rate = 48.51% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.8116 >>>>>>> ACTG content number of A's = 2,456,336,013 bp (26.09%) number of C's = 2,206,201,751 bp (23.43%) number of T's = 2,478,378,152 bp (26.32%) number of G's = 2,217,644,852 bp (23.56%) number of N's = 56,109,208 bp (0.6%) GC percentage = 46.99% >>>>>>> Mismatches and indels general error rate = 0.0102 number of mismatches = 89,886,542 number of insertions = 3,522,152 mapped reads with insertion percentage = 3.35% number of deletions = 2,752,305 mapped reads with deletion percentage = 2.65% homopolymer indels = 41.74% >>>>>>> Coverage mean coverageData = 3.0433X std coverageData = 110.1661X There is a 6.35% of reference with a coverageData >= 1X There is a 3.83% of reference with a coverageData >= 2X There is a 2.91% of reference with a coverageData >= 3X There is a 2.51% of reference with a coverageData >= 4X There is a 2.26% of reference with a coverageData >= 5X There is a 2.09% of reference with a coverageData >= 6X There is a 1.95% of reference with a coverageData >= 7X There is a 1.85% of reference with a coverageData >= 8X There is a 1.76% of reference with a coverageData >= 9X There is a 1.69% of reference with a coverageData >= 10X There is a 1.62% of reference with a coverageData >= 11X There is a 1.56% of reference with a coverageData >= 12X There is a 1.51% of reference with a coverageData >= 13X There is a 1.46% of reference with a coverageData >= 14X There is a 1.42% of reference with a coverageData >= 15X There is a 1.38% of reference with a coverageData >= 16X There is a 1.34% of reference with a coverageData >= 17X There is a 1.31% of reference with a coverageData >= 18X There is a 1.28% of reference with a coverageData >= 19X There is a 1.24% of reference with a coverageData >= 20X There is a 1.22% of reference with a coverageData >= 21X There is a 1.19% of reference with a coverageData >= 22X There is a 1.16% of reference with a coverageData >= 23X There is a 1.14% of reference with a coverageData >= 24X There is a 1.11% of reference with a coverageData >= 25X There is a 1.09% of reference with a coverageData >= 26X There is a 1.07% of reference with a coverageData >= 27X There is a 1.05% of reference with a coverageData >= 28X There is a 1.03% of reference with a coverageData >= 29X There is a 1.01% of reference with a coverageData >= 30X There is a 0.99% of reference with a coverageData >= 31X There is a 0.98% of reference with a coverageData >= 32X There is a 0.96% of reference with a coverageData >= 33X There is a 0.94% of reference with a coverageData >= 34X There is a 0.93% of reference with a coverageData >= 35X There is a 0.91% of reference with a coverageData >= 36X There is a 0.9% of reference with a coverageData >= 37X There is a 0.89% of reference with a coverageData >= 38X There is a 0.87% of reference with a coverageData >= 39X There is a 0.86% of reference with a coverageData >= 40X There is a 0.85% of reference with a coverageData >= 41X There is a 0.83% of reference with a coverageData >= 42X There is a 0.82% of reference with a coverageData >= 43X There is a 0.81% of reference with a coverageData >= 44X There is a 0.8% of reference with a coverageData >= 45X There is a 0.79% of reference with a coverageData >= 46X There is a 0.78% of reference with a coverageData >= 47X There is a 0.77% of reference with a coverageData >= 48X There is a 0.76% of reference with a coverageData >= 49X There is a 0.75% of reference with a coverageData >= 50X There is a 0.74% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 869127505 3.4869622451211466 124.91465603269587 chr2 243199373 758914487 3.120544587094803 132.91732587835392 chr3 198022430 836190496 4.22270596315781 122.47913195616006 chr4 191154276 964052361 5.04332092994875 81.68802975659989 chr5 180915260 205713973 1.1370736387853628 40.20749040277381 chr6 171115067 156157446 0.9125873526964169 35.693493406654966 chr7 159138663 298984107 1.878764728593956 37.75475076451484 chr8 146364022 397482311 2.7157104974882422 150.9351877685161 chr9 141213431 89698003 0.6351945587951899 30.280356258453285 chr10 135534747 2156385153 15.910201632648489 303.2083939373314 chr11 135006516 237569625 1.7596900656261658 38.13983889293003 chr12 133851895 499634545 3.7327416619689995 125.5246842803079 chr13 115169878 56953369 0.4945161876441338 22.155115008186073 chr14 107349540 282655522 2.633038967842806 59.148051215779944 chr15 102531392 130732891 1.27505233714178 109.32696145826125 chr16 90354753 154089314 1.7053813870754535 93.75589036524556 chr17 81195210 176339776 2.171800233043304 28.247882908852258 chr18 78077248 113062103 1.448080021980283 33.29985615920278 chr19 59128983 209719663 3.5468166770262224 125.64979827340784 chr20 63025520 284658647 4.516561656294149 132.58532056571423 chr21 48129895 164333204 3.4143686372056288 110.39282047924698 chr22 51304566 305465378 5.953960861885081 123.19240657293017 chrMT 16571 4299095 259.43485607386395 160.37420743265463 chrX 155270560 43743474 0.28172419807077403 13.022422529928523 chrY 59373566 25123580 0.42314419854788576 41.953858380069676