BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819124.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 = 5,678,028 number of mapped reads = 5,170,660 (91.06%) number of supplementary alignments = 17,847 (0.31%) number of secondary alignments = 0 number of mapped bases = 301,154,145 bp number of sequenced bases = 301,056,993 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 424,605 duplication rate = 5.91% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7698 >>>>>>> ACTG content number of A's = 74,154,255 bp (24.63%) number of C's = 61,740,870 bp (20.51%) number of T's = 91,399,965 bp (30.36%) number of G's = 73,757,727 bp (24.5%) number of N's = 4,176 bp (0%) GC percentage = 45.01% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 1,542,879 number of insertions = 20,058 mapped reads with insertion percentage = 0.39% number of deletions = 57,986 mapped reads with deletion percentage = 1.11% homopolymer indels = 43.53% >>>>>>> Coverage mean coverageData = 0.0973X std coverageData = 0.7814X There is a 7.43% of reference with a coverageData >= 1X There is a 1.51% of reference with a coverageData >= 2X There is a 0.38% of reference with a coverageData >= 3X There is a 0.12% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 0.01% 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 29779562 0.11947638036175645 1.6604714397795406 chr2 243199373 23727973 0.09756592999111063 0.8927299072330346 chr3 198022430 16456699 0.08310522701897961 0.3737031127904297 chr4 191154276 16872714 0.08826752062820714 0.4752207264268122 chr5 180915260 16388669 0.09058754358255904 0.38656830150488597 chr6 171115067 12803426 0.07482348705155227 0.5601429254204213 chr7 159138663 15082169 0.09477375714787802 1.0497672995825609 chr8 146364022 27544838 0.18819404949120624 0.7544029312067788 chr9 141213431 12803968 0.09067103539181057 0.6160229182796986 chr10 135534747 15893479 0.11726497707632125 0.7745842179389446 chr11 135006516 10261388 0.07600661289563239 0.6970470780330976 chr12 133851895 14059758 0.10503966342800003 0.4184381411228543 chr13 115169878 6707010 0.058235800162955806 0.31081108068224356 chr14 107349540 7116797 0.06629555189523867 0.34448076199072886 chr15 102531392 8011539 0.07813742546282801 0.3755989608055202 chr16 90354753 9488354 0.10501222885308535 0.49099233833654193 chr17 81195210 10679494 0.13152862096175377 0.5210933654840849 chr18 78077248 7072349 0.09058143289066746 1.287229537733006 chr19 59128983 6306040 0.1066488831712191 1.1250289993818081 chr20 63025520 8655908 0.1373397315880932 0.48638071001404 chr21 48129895 4136902 0.08595285736650786 0.4500972346090355 chr22 51304566 2483808 0.048413000901323285 0.2783147747678743 chrMT 16571 26544 1.6018345302033674 1.8393165535233644 chrX 155270560 17830628 0.11483585813047882 0.5451432217419001 chrY 59373566 964129 0.0162383542871587 0.42956704171307786