BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708634.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 3,579,839 number of mapped reads = 2,561,348 (71.55%) number of supplementary alignments = 832 (0.02%) number of secondary alignments = 0 number of mapped bases = 124,699,558 bp number of sequenced bases = 124,674,904 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 90,506 duplication rate = 2.42% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.1802 >>>>>>> ACTG content number of A's = 36,886,523 bp (29.59%) number of C's = 23,360,815 bp (18.74%) number of T's = 39,484,256 bp (31.67%) number of G's = 24,932,438 bp (20%) number of N's = 10,872 bp (0.01%) GC percentage = 38.74% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 803,901 number of insertions = 5,838 mapped reads with insertion percentage = 0.23% number of deletions = 16,045 mapped reads with deletion percentage = 0.62% homopolymer indels = 47.51% >>>>>>> Coverage mean coverageData = 0.0403X std coverageData = 0.3975X There is a 3.48% of reference with a coverageData >= 1X There is a 0.4% of reference with a coverageData >= 2X There is a 0.06% 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 9681448 0.0388422221824675 0.7826406759245658 chr2 243199373 10920896 0.0449051157710016 0.40357775358391107 chr3 198022430 8227630 0.04154898008271083 0.23338312943866868 chr4 191154276 8494233 0.044436531464250376 0.24282686002390816 chr5 180915260 7948679 0.0439359233709749 0.2417729780090258 chr6 171115067 7544708 0.044091430008322996 0.31007775527795545 chr7 159138663 7198987 0.045237196695563545 0.5574464122771347 chr8 146364022 6486476 0.04431742112142832 0.5731319223755243 chr9 141213431 5366556 0.03800315566300489 0.32789312162050993 chr10 135534747 5668215 0.04182112060164173 0.31017152972273393 chr11 135006516 5433656 0.04024736109774139 0.3217096113045022 chr12 133851895 5488609 0.04100508999144166 0.2349886715143133 chr13 115169878 4250875 0.036909607562491294 0.21778221511998067 chr14 107349540 3864695 0.03600103922196592 0.23110306270444447 chr15 102531392 3561725 0.03473789763821796 0.2117334677623475 chr16 90354753 3083128 0.03412247720936164 0.22580747601652762 chr17 81195210 2997331 0.03691512097819564 0.25291270355240636 chr18 78077248 3502793 0.0448631719191742 0.6776249724733349 chr19 59128983 2066519 0.03494934117165519 0.5638475390873081 chr20 63025520 2373843 0.03766479038967072 0.22859200500485508 chr21 48129895 1654169 0.03436884705441389 0.23280363154746217 chr22 51304566 1130212 0.022029462250981714 0.1654421026248384 chrMT 16571 4449 0.2684810814072778 0.5875484523034481 chrX 155270560 7424950 0.047819432093244206 0.28062367801013044 chrY 59373566 324776 0.005470043689139372 0.10478076377899898